diff --git a/inc/config.h b/inc/config.h
--- a/inc/config.h
+++ b/inc/config.h
@@ -2,18 +2,17 @@
 #define CONFIG_H
 
 
+//////////////////////////////////////////////////////
+// Sensor Type
+//////////////////////////////////////////////////////
+//#define MAX31855_TC_SENSOR
+//#define MAX31865_RTD_SENSOR
+#define MAX_WHATEVERTHENEWONEIS
+
 
 //////////////////////////////////////////////////////
-// Watchdog Settings
+// USB
 //////////////////////////////////////////////////////
-//#define WATCHDOG_ENABLE
-
-
-
-// Temperature sensor type
-#define MAX31855_TC_SENSOR
-//#define MAX31865_RTD_SENSOR
-
 
 // Virtual serial port transmit rate
 #define VCP_TX_FREQ 1000
@@ -25,18 +24,18 @@
 #define PID_PERIOD 120
 
 
-
-// Pin settings
-#define LED_POWER GPIOF,GPIO_PIN_0
-#define MAX_CS GPIOA,GPIO_PIN_15
-
-#define SSR_PIN GPIOA, GPIO_PIN_1
-
+//////////////////////////////////////////////////////
+// Other settings
+//////////////////////////////////////////////////////
 
 // Add bootloader option to top of idle screen menu
 #define BOOTLOADER_SHORTCUT
 
 
+//////////////////////////////////////////////////////
+// Default Settings
+//////////////////////////////////////////////////////
+
 #define DEFAULT_BOOT_TO_BREW 0
 #define DEFAULT_TEMP_UNITS TEMP_UNITS_FAHRENHEIT
 #define DEFAULT_WINDUP_GUARD 10
@@ -50,6 +49,12 @@
 #define DEFAULT_HYSTERESIS 1
 
 
+//////////////////////////////////////////////////////
+// Watchdog Settings
+//////////////////////////////////////////////////////
+//#define WATCHDOG_ENABLE
+
+
 
 // Internal macros
 #define hal_init HAL_Init
diff --git a/inc/display.h b/inc/display.h
--- a/inc/display.h
+++ b/inc/display.h
@@ -8,6 +8,6 @@
 #endif
 
 void display_startup_screen();
-void display_process(therm_settings_t* set, therm_status_t* status);
+void display_process(therm_status_t* status);
 
 #endif
diff --git a/inc/system/flash.h b/inc/system/flash.h
--- a/inc/system/flash.h
+++ b/inc/system/flash.h
@@ -1,23 +1,16 @@
 #ifndef flash_h
 #define flash_h
 
+#include "states.h"
+
 #define FLASH_MAGIC_LOC 511
 #define FLASH_MAGIC_VALUE 0xbeef
 
 
-typedef union
-{
-	struct _values {
-		uint16_t can_id;
-		uint16_t tx_period;
-	} values;
-
-	uint16_t data[128];
-} settings_t;
 
 void flash_init(void);
 void flash_savesettings(void);
 void flash_restoresettings(void);
-settings_t* flash_getsettings(void);
+therm_settings_t* flash_getsettings(void);
 
 #endif // flash_h
diff --git a/inc/system/gpio.h b/inc/system/gpio.h
--- a/inc/system/gpio.h
+++ b/inc/system/gpio.h
@@ -29,6 +29,7 @@
 #define LED_GPIO_Port GPIOB
 #define LED LED_GPIO_Port, LED_PIN
 
+/// SSR PIN ???///
 
 void user_input(uint16_t* to_modify);
 void user_input_signed(int32_t* to_modify);
diff --git a/inc/stm32f3xx_hal_conf.h b/inc/system/stm32f3xx_hal_conf.h
rename from inc/stm32f3xx_hal_conf.h
rename to inc/system/stm32f3xx_hal_conf.h
diff --git a/lib/ssd1306/ssd1306.c b/lib/ssd1306/ssd1306.c
--- a/lib/ssd1306/ssd1306.c
+++ b/lib/ssd1306/ssd1306.c
@@ -5,7 +5,7 @@
 SPI_HandleTypeDef hspi1;
 
 
-
+// SPI handle accessor
 SPI_HandleTypeDef* spi_get()
 {
     return &hspi1;
@@ -33,80 +33,79 @@ static void WriteData(unsigned char data
 // Initialize OLED
 void ssd1306_init(void)
 {
-    __SPI3_CLK_ENABLE();
-    __GPIOA_CLK_ENABLE();
-    __GPIOB_CLK_ENABLE();
-    GPIO_InitTypeDef GPIO_InitStruct;
+	__SPI3_CLK_ENABLE();
+	__GPIOA_CLK_ENABLE();
+	__GPIOB_CLK_ENABLE();
+	GPIO_InitTypeDef GPIO_InitStruct;
 
-    /*Configure GPIO pins : OLED_CS_Pin OLED_RESET_Pin OLED_DC_Pin */
-    GPIO_InitStruct.Pin = OLED_CS_Pin|OLED_RESET_Pin|OLED_DC_Pin;
-    GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
-    GPIO_InitStruct.Pull = GPIO_NOPULL;
-    GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
-    HAL_GPIO_Init(OLED_DC_GPIO_Port, &GPIO_InitStruct);
+	/*Configure GPIO pins : OLED_CS_Pin OLED_RESET_Pin OLED_DC_Pin */
+	GPIO_InitStruct.Pin = OLED_CS_Pin|OLED_RESET_Pin|OLED_DC_Pin;
+	GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
+	GPIO_InitStruct.Pull = GPIO_NOPULL;
+	GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
+	HAL_GPIO_Init(OLED_DC_GPIO_Port, &GPIO_InitStruct);
 
 
 	// Set up MOSI/MISO/SCK
-    GPIO_InitStruct.Pin = GPIO_PIN_3|GPIO_PIN_4|GPIO_PIN_5;
-    GPIO_InitStruct.Mode = GPIO_MODE_AF_PP;
-    GPIO_InitStruct.Pull = GPIO_NOPULL;
-    GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
-    GPIO_InitStruct.Alternate = GPIO_AF6_SPI3;
-    HAL_GPIO_Init(GPIOB, &GPIO_InitStruct);
+	GPIO_InitStruct.Pin = GPIO_PIN_3|GPIO_PIN_4|GPIO_PIN_5;
+	GPIO_InitStruct.Mode = GPIO_MODE_AF_PP;
+	GPIO_InitStruct.Pull = GPIO_NOPULL;
+	GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
+	GPIO_InitStruct.Alternate = GPIO_AF6_SPI3;
+	HAL_GPIO_Init(GPIOB, &GPIO_InitStruct);
 
 
 	// Set up SPI port for OLED
-    hspi1.Instance = SPI3;
-    hspi1.Init.Mode = SPI_MODE_MASTER;
-    hspi1.Init.Direction = SPI_DIRECTION_2LINES;
-    hspi1.Init.DataSize = SPI_DATASIZE_8BIT;
-    hspi1.Init.CLKPolarity = SPI_POLARITY_LOW;
-    hspi1.Init.CLKPhase = SPI_PHASE_1EDGE;
-    hspi1.Init.NSS = SPI_NSS_SOFT;
-    hspi1.Init.BaudRatePrescaler = SPI_BAUDRATEPRESCALER_16;
-    hspi1.Init.FirstBit = SPI_FIRSTBIT_MSB;
-    hspi1.Init.TIMode = SPI_TIMODE_DISABLED;
-    hspi1.Init.CRCCalculation = SPI_CRCCALCULATION_DISABLED;
-    hspi1.Init.NSSPMode = SPI_NSS_PULSE_ENABLED;
-    HAL_SPI_Init(&hspi1);
-
+	hspi1.Instance = SPI3;
+	hspi1.Init.Mode = SPI_MODE_MASTER;
+	hspi1.Init.Direction = SPI_DIRECTION_2LINES;
+	hspi1.Init.DataSize = SPI_DATASIZE_8BIT;
+	hspi1.Init.CLKPolarity = SPI_POLARITY_LOW;
+	hspi1.Init.CLKPhase = SPI_PHASE_1EDGE;
+	hspi1.Init.NSS = SPI_NSS_SOFT;
+	hspi1.Init.BaudRatePrescaler = SPI_BAUDRATEPRESCALER_16;
+	hspi1.Init.FirstBit = SPI_FIRSTBIT_MSB;
+	hspi1.Init.TIMode = SPI_TIMODE_DISABLED;
+	hspi1.Init.CRCCalculation = SPI_CRCCALCULATION_DISABLED;
+	hspi1.Init.NSSPMode = SPI_NSS_PULSE_ENABLED;
+	HAL_SPI_Init(&hspi1);
 
 
-  /* Generate a reset */
-  SSD_Reset_Low();
-  uint32_t i;
-  for(i=5000; i>1; i--)
-  SSD_Reset_High();
+	// Generate a reset
+	SSD_Reset_Low();
+	uint32_t i;
+	for(i=5000; i>1; i--)
+	SSD_Reset_High();
 
-  WriteCommand(0xAE);
-  WriteCommand(0xD5);
-  WriteCommand(0x80);
-  WriteCommand(0xA8);
-  WriteCommand(0x1F);
-  WriteCommand(0xD3);
-  WriteCommand(0x00);
-  WriteCommand(0x40 | 0x00); // line #0
-  WriteCommand(0x8D);
-  WriteCommand(0x14); //10 or 14 if not externalvcc
-  WriteCommand(0x20);
-  WriteCommand(0x00);
-//  WriteCommand(0xA0 | 0x1); // segremap (normal)
-  WriteCommand(0xA0); // segremap (flip)
-//  WriteCommand(0xC8); // comscandec (normal)
-  WriteCommand(0xC0); // comscandec (flip)
-  WriteCommand(0xDA); // setcompins
-  WriteCommand(0x02);
-  WriteCommand(0x81); // contrast
-  WriteCommand(0x0F); // contrast value. 8f is a good one.
-  WriteCommand(0xD9);
-  WriteCommand(0xF1); //22 or F1 if not externalvcc
-  WriteCommand(0xDB);
-  WriteCommand(0x40);
-  WriteCommand(0xA4); // dispalyallon_resume
-  WriteCommand(0xA6); // normaldisplay
+	WriteCommand(0xAE);
+	WriteCommand(0xD5);
+	WriteCommand(0x80);
+	WriteCommand(0xA8);
+	WriteCommand(0x1F);
+	WriteCommand(0xD3);
+	WriteCommand(0x00);
+	WriteCommand(0x40 | 0x00); // line #0
+	WriteCommand(0x8D);
+	WriteCommand(0x14); //10 or 14 if not externalvcc
+	WriteCommand(0x20);
+	WriteCommand(0x00);
+	//  WriteCommand(0xA0 | 0x1); // segremap (normal)
+	WriteCommand(0xA0); // segremap (flip)
+	//  WriteCommand(0xC8); // comscandec (normal)
+	WriteCommand(0xC0); // comscandec (flip)
+	WriteCommand(0xDA); // setcompins
+	WriteCommand(0x02);
+	WriteCommand(0x81); // contrast
+	WriteCommand(0x0F); // contrast value. 8f is a good one.
+	WriteCommand(0xD9);
+	WriteCommand(0xF1); //22 or F1 if not externalvcc
+	WriteCommand(0xDB);
+	WriteCommand(0x40);
+	WriteCommand(0xA4); // dispalyallon_resume
+	WriteCommand(0xA6); // normaldisplay
 
 
-  WriteCommand(0xAF); // display on
+	WriteCommand(0xAF); // display on
 }
 
 
@@ -228,12 +227,15 @@ static const char fontData[][5] =
 };
 
 
+// Set start page
 static void setStartPage(unsigned char d)
 {
     WriteCommand(0xB0|d);       // Set Page Start Address for Page Addressing Mode
                                 // Default => 0xB0 (0x00)
 }
-/* Below are functions used to configure the OLED */
+
+
+// Set start column
 static void setStartColumn(unsigned char d)
 {
     WriteCommand(0x00+d%16);    // Set Lower Column Start Address for Page Addressing Mode
@@ -242,6 +244,7 @@ static void setStartColumn(unsigned char
 }
 
 
+// Therm logo
 const uint8_t row[4][32] = {
 
 	{0x00,0x00,0x01,0x03,0x07,0x0F,0x1E,0x3C,0x3C,0x7C,0x7C,0x7C,0xFC,0xFF,0xFF,0xFC,0xFC,0xFC,0xFC,0xFF,0x7F,0x7F,0x7F,0x3C,0x3C,0x1C,0x0C,0x06,0x03,0x01,0x00,0x00},
@@ -254,6 +257,8 @@ const uint8_t row[4][32] = {
 
 };
 
+
+// Clear the screen
 void ssd1306_clearscreen()
 {
     uint8_t i = 0;
@@ -270,6 +275,8 @@ void ssd1306_clearscreen()
     WriteData(0x00);
 }
 
+
+// Draw the therm logo on the left side of the OLED
 void ssd1306_drawlogo()
 {
     uint8_t i = 0;
@@ -307,7 +314,8 @@ void ssd1306_drawlogo()
     WriteData(0x00);
 }
 
-/* Print a single character from font.cpp */
+
+// Print a single character
 void ssd1306_drawchar(char ascii, unsigned char row, unsigned char xPos)
 {
     const char *srcPointer = (char*)-1;
@@ -325,6 +333,8 @@ void ssd1306_drawchar(char ascii, unsign
     WriteData(0x00);
 }
 
+
+// Print a single large character
 void ssd1306_drawcharbig(char ascii, unsigned char row, unsigned char xPos)
 {
     const char *srcPointer = (char*)-1;
@@ -387,6 +397,8 @@ void ssd1306_drawcharbig(char ascii, uns
 
 }
 
+
+// Print a string to the display
 void ssd1306_drawstring(const char *dataPtr, unsigned char row, unsigned char xPos)
 {
     char *srcPointer;
@@ -404,6 +416,7 @@ void ssd1306_drawstring(const char *data
 }
 
 
+// Print a string to the display, big font
 void ssd1306_drawstringbig(const char *dataPtr, unsigned char row, unsigned char xPos)
 {
     char *srcPointer;
diff --git a/src/display.c b/src/display.c
--- a/src/display.c
+++ b/src/display.c
@@ -1,3 +1,7 @@
+//
+// Display: render menus on OLED display
+//
+
 #include "display.h"
 #include "gpio.h"
 #include "ssd1306/ssd1306.h"
@@ -35,8 +39,9 @@ static uint8_t reset_mode = RESET_REBOOT
 
 
 // Display state machine
-void display_process(therm_settings_t* set, therm_status_t* status)
+void display_process(therm_status_t* status)
 {
+	therm_settings_t* set = flash_getsettings();
     uint8_t state_changed = status->state != last_state;
     last_state = status->state;
     
diff --git a/src/main.c b/src/main.c
--- a/src/main.c
+++ b/src/main.c
@@ -18,7 +18,6 @@
 #include "interrupts.h"
 
 
-therm_settings_t set;
 therm_status_t status;
 pid_state_t pid_state;
 
@@ -38,15 +37,7 @@ int main(void)
 
 	ssd1306_drawlogo();
 
-	watchdog_init();
 
-	//just some example code for getting flash values
-//	flash_getsettings()->values.can_id = 67;
-//
-//	if(flash_getsettings()->values.can_id == 12);
-
-//	ssd1306_drawstring(const char *dataPtr, unsigned char row, unsigned char xPos)
-//	ssd1306_drawstring("[ ProtoFuse ]", 0, 0);
 
     // Default status
     status.temp = 0;
@@ -59,15 +50,10 @@ int main(void)
     pid_init(&pid_state);
 
     flash_init();
+	watchdog_init();
 
 
-	float temp_counter = 0;
-
-	// Software timers
-	uint32_t last_screen_update_time = HAL_GetTick();
-
-
-    // Soft timers
+	// Soft timers
     uint32_t last_ssr_on = 0;
     uint32_t last_vcp_tx = 0;
     uint32_t last_led = 0;
@@ -80,7 +66,7 @@ int main(void)
 	while (1)
 	{
 
-        if(set.val.control_mode == MODE_PID && (HAL_GetTick() - last_pid > PID_PERIOD))
+        if(flash_getsettings()->val.control_mode == MODE_PID && (HAL_GetTick() - last_pid > PID_PERIOD))
         {
 
 //            #ifdef MAX31865_RTD_SENSOR
@@ -93,9 +79,9 @@ int main(void)
             if(status.pid_enabled)
             {
                 // Get ssr output for next time
-                int16_t power_percent = pid_update(&set, &status, &pid_state);
+                int16_t power_percent = pid_update(flash_getsettings(), &status, &pid_state);
 
-                if(set.val.plant_type == PLANT_HEATER)
+                if(flash_getsettings()->val.plant_type == PLANT_HEATER)
                     power_percent *= -1;
 
                 //power-percent is 0-1000?
@@ -144,7 +130,7 @@ int main(void)
 
 
         // Thermostatic control
-        if(set.val.control_mode == MODE_THERMOSTAT && HAL_GetTick() - last_thermostat > SSR_PERIOD)
+        if(flash_getsettings()->val.control_mode == MODE_THERMOSTAT && HAL_GetTick() - last_thermostat > SSR_PERIOD)
         {
 
 //            #ifdef MAX31865_RTD_SENSOR
@@ -160,14 +146,14 @@ int main(void)
 
 
             // EMZ FIXME: This could be way simpler
-            if(set.val.plant_type == PLANT_HEATER && status.setpoint * 10 < temp - set.val.hysteresis * 10)
+            if(flash_getsettings()->val.plant_type == PLANT_HEATER && status.setpoint * 10 < temp - flash_getsettings()->val.hysteresis * 10)
                 thermostat_plant_on = 1;
-            else if(set.val.plant_type == PLANT_HEATER && status.setpoint * 10 > temp + set.val.hysteresis * 10)
+            else if(flash_getsettings()->val.plant_type == PLANT_HEATER && status.setpoint * 10 > temp + flash_getsettings()->val.hysteresis * 10)
                 thermostat_plant_on = 0;
 
-            if(set.val.plant_type == PLANT_COOLER && status.setpoint * 10 > temp + set.val.hysteresis * 10)
+            if(flash_getsettings()->val.plant_type == PLANT_COOLER && status.setpoint * 10 > temp + flash_getsettings()->val.hysteresis * 10)
                 thermostat_plant_on = 1;
-            else if(set.val.plant_type == PLANT_COOLER && status.setpoint * 10 < temp - set.val.hysteresis * 10)
+            else if(flash_getsettings()->val.plant_type == PLANT_COOLER && status.setpoint * 10 < temp - flash_getsettings()->val.hysteresis * 10)
                 thermostat_plant_on = 0;
 
             // EMZ: TODO: Refactor to output_enabled or something
@@ -182,13 +168,13 @@ int main(void)
 
 
 
-                HAL_GPIO_WritePin(SSR_PIN, 1);
-                HAL_GPIO_WritePin(LED_POWER, 1);
+//                HAL_GPIO_WritePin(SSR_PIN, 1);
+                HAL_GPIO_WritePin(LED, 1);
             }
             else
             {
-                HAL_GPIO_WritePin(SSR_PIN, 0);
-                HAL_GPIO_WritePin(LED_POWER, 0);
+//                HAL_GPIO_WritePin(SSR_PIN, 0);
+                HAL_GPIO_WritePin(LED, 0);
             }
 
             last_thermostat = HAL_GetTick();
@@ -213,7 +199,7 @@ int main(void)
 //        }
 
         // Run state machine
-        display_process(&set, &status);
+        display_process(&status);
 
 		watchdog_feed();
 	}
diff --git a/src/pid.c b/src/pid.c
--- a/src/pid.c
+++ b/src/pid.c
@@ -1,3 +1,7 @@
+//
+// PID: proportional/integral/derivative controller
+//
+
 #include "pid.h"
 
 // PID implementation
diff --git a/src/system/flash.c b/src/system/flash.c
--- a/src/system/flash.c
+++ b/src/system/flash.c
@@ -8,8 +8,8 @@
 
 // Takes up 1 page (1k size)
 static __attribute__((__section__(".eeprom"))) uint16_t eeprom_emulation[512];
-settings_t settings;
 
+therm_settings_t settings;
 
 // Initialize flash and restore settings
 void flash_init(void)
@@ -19,7 +19,7 @@ void flash_init(void)
 
 
 // Save settings to flash memory
-void flash_savesettings(void)
+void flash_savesettings()
 {
 	// Unlock flash memory
 	HAL_FLASH_Unlock();
@@ -68,13 +68,13 @@ void flash_restoresettings(void)
 	// No data in flash! Set defaults here
 	else
 	{
-		settings.values.can_id = 22;
+		//torestore.values.can_id = 22;
 	}
 }
 
 
 // Accessor to retrieve settings structure
-inline settings_t* flash_getsettings(void)
+inline therm_settings_t* flash_getsettings(void)
 {
 	return &settings;
 }