diff --git a/flight/sys/pios_irq.h b/flight/sys/pios_irq.h
index d074ecc03..dd288681b 100644
--- a/flight/sys/pios_irq.h
+++ b/flight/sys/pios_irq.h
@@ -28,7 +28,7 @@
 #ifndef PIOS_IRQ_H
 #define PIOS_IRQ_H
 
-/* Function Prototypes */
+/* Public Functions */
 extern void UARTInit(void);
 extern void EnableAuxUART(void);
 extern void DisableAuxUART(void);
diff --git a/flight/sys/pios_led.h b/flight/sys/pios_led.h
index c8de746eb..bd3509df1 100644
--- a/flight/sys/pios_led.h
+++ b/flight/sys/pios_led.h
@@ -31,7 +31,7 @@
 /* Type Definitions */
 typedef enum {LED1 = 0, LED2 = 1} LedTypeDef;
 
-/* Exported Functions */
+/* Public Functions */
 extern void LED_INIT(void);
 extern void LED_ON(LedTypeDef LEDNum);
 extern void LED_OFF(LedTypeDef LEDNum);
diff --git a/flight/sys/pios_settings.c b/flight/sys/pios_settings.c
index aa240b412..e506b2034 100644
--- a/flight/sys/pios_settings.c
+++ b/flight/sys/pios_settings.c
@@ -25,15 +25,35 @@
  * 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  */
 
+
 /* Project Includes */
 #include "pios.h"
 
+
+/* Public Function Prototypes */
+void LoadSettings(void);
+
+
+/* Private Function Prototypes */
+
+
 /* Local Variables */
 SettingsTypeDef Settings;
 
-/* Loads Settings from INI file 																			*/
+
+/*******************************************************************************
+* Function Name  : LoadSettings
+* Description    : Populate System global Vars into Structs using MinIni, 
+* 		 : defaults are also set here. Only function in the file
+*		 : and where all our system data is handled. 
+*		 : Called from the end of SysInit()		   
+* Input          : None
+* Output         : None
+* Return         : None
+*******************************************************************************/
 /* Value Reading:	ini_getl("Section", "Key", (DefaultValue), IniFile);									*/
 /* String Reading:	ini_gets("Section", "Key", "DefaultValue", StrBuffer, sizearray(StrBuffer), IniFile); 	*/
+
 void LoadSettings(void)
 {
 	char StrBuffer[100];
diff --git a/flight/sys/pios_settings.h b/flight/sys/pios_settings.h
index 343422c8a..938dcb18a 100644
--- a/flight/sys/pios_settings.h
+++ b/flight/sys/pios_settings.h
@@ -57,10 +57,10 @@ typedef struct {
 	UARTSettingsTypeDef AuxUART;
 } SettingsTypeDef;
 
-/*Global Veriables */
+/*Global Variables */
 extern SettingsTypeDef Settings;
 
-/* Function Prototypes */
+/* Public Functions */
 extern void LoadSettings(void);
 
 #endif /* PIOS_SETTINGS_H */
\ No newline at end of file
diff --git a/flight/sys/pios_sys.c b/flight/sys/pios_sys.c
index 4368aeed0..989f7e5c1 100644
--- a/flight/sys/pios_sys.c
+++ b/flight/sys/pios_sys.c
@@ -25,12 +25,31 @@
  * 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  */
 
+
 /* Project Includes */
 #include "pios.h"
 
+
+/* Public Function Prototypes */
+void SysInit(void);
+
+
+/* Private Function Prototypes */
+void NVIC_Configuration(void);
+
+
 /* Local Variables */
 FATFS Fatfs[_DRIVES];	// File system object for each logical drive */
 
+
+/*******************************************************************************
+* Function Name  : SysInit
+* Description    : Brings up the System and Initializes peripherals 
+* Input          : None
+* Output         : None
+* Return         : None
+*******************************************************************************/
+//TODO: Get these in the right order, settings need to be loaded ASAP
 void SysInit(void)
 {
 	/* Setup STM32 system (RCC, clock, PLL and Flash configuration) - CMSIS Function */
@@ -51,13 +70,15 @@ void SysInit(void)
 		}
 	}
 	
+	/* Call LoadSettings which populates System Vars */
 	LoadSettings();
 	
 }
 
+
 /*******************************************************************************
 * Function Name  : GPIO_Configuration
-* Description    : Configures the different GPIO ports.
+* Description    : Configures base level GPIO ports.
 * Input          : None
 * Output         : None
 * Return         : None
@@ -67,9 +88,10 @@ void GPIO_Configuration(void)
 
 }
 
+
 /*******************************************************************************
 * Function Name  : NVIC_Configuration
-* Description    : Configures Vector Table base location.
+* Description    : Configures Vector Table base location and SysTick
 * Input          : None
 * Output         : None
 * Return         : None
@@ -78,6 +100,8 @@ void NVIC_Configuration(void)
 {
 	/* Set the Vector Table base address as specified in .ld file */
 	NVIC_SetVectorTable(NVIC_VectTab_FLASH, 0x0);
+
+	/* 4 bits for Interupt priorities so no sub priorities */
 	NVIC_PriorityGroupConfig(NVIC_PriorityGroup_4);
 
 	/* Configure HCLK clock as SysTick clock source. */
diff --git a/flight/sys/pios_sys.h b/flight/sys/pios_sys.h
index 745bbd921..f1796d1e3 100644
--- a/flight/sys/pios_sys.h
+++ b/flight/sys/pios_sys.h
@@ -28,9 +28,7 @@
 #ifndef PIOS_SYS_H
 #define PIOS_SYS_H
 
-/* Exported Functions */
+/* Public Functions */
 extern void SysInit(void);
-extern void GPIO_Configuration(void);
-extern void NVIC_Configuration(void);
 
 #endif /* PIOS_SYS_H */
diff --git a/flight/sys/pios_uart.c b/flight/sys/pios_uart.c
index e790f8917..0c00c1ff1 100644
--- a/flight/sys/pios_uart.c
+++ b/flight/sys/pios_uart.c
@@ -5,7 +5,7 @@
  * @author The OpenPilot Team, http://www.openpilot.org, Copyright (C) 2009.
  *    
  * @file pios_uart.c
- * UART commands, Inits UARTS, controls & talks to UARTS
+ * UART commands. Inits USARTs, controls UARTs & Interupt handlers
  *
  * @see The GNU Public License (GPL)
  */
@@ -25,9 +25,21 @@
  * 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  */
 
+
 /* Project Includes */
 #include "pios.h"
 
+
+/* Public Function Prototypes */
+void UARTInit(void);
+void EnableAuxUART(void);
+void DisableAuxUART(void);
+void UARTChangeBaud(USART_TypeDef* USARTx, uint32_t Baud);
+
+
+/* Private Function Prototypes */
+
+
 /* Local Variables */
 static u8 rx_buffer[UART_NUM][UART_RX_BUFFER_SIZE];
 static volatile u8 rx_buffer_tail[UART_NUM];
@@ -39,7 +51,14 @@ static volatile u8 tx_buffer_tail[UART_NUM];
 static volatile u8 tx_buffer_head[UART_NUM];
 static volatile u8 tx_buffer_size[UART_NUM];
 
-/* Initialise the GPS and TELEM onboard UARTs */
+
+/*******************************************************************************
+* Function Name  : UARTInit
+* Description    : Initialise the GPS and TELEM onboard UARTs
+* Input          : None
+* Output         : None
+* Return         : None
+*******************************************************************************/
 void UARTInit(void)
 {
 	GPIO_InitTypeDef GPIO_InitStructure;
@@ -129,17 +148,41 @@ void UARTInit(void)
 	}
 }
 
+
+/*******************************************************************************
+* Function Name  : EnableAuxUART
+* Description    : Enables AUX UART at the expense of servo inputs
+* Input          : None
+* Output         : None
+* Return         : None
+*******************************************************************************/
 void EnableAuxUART(void)
 {
 	//Implement after servo inputs are implemented
 }
 
+
+/*******************************************************************************
+* Function Name  : DisableAuxUART
+* Description    : Disables AUX UART reclaims two servo inputs
+* Input          : None
+* Output         : None
+* Return         : None
+*******************************************************************************/
 void DisableAuxUART(void)
 {
 	//Implement after servo inputs are implemented
 }
 
-/* Changes the baud rate of the USART peripherial without re-initialising */
+
+/*******************************************************************************
+* Function Name  : UARTInit
+* Description    : Changes the baud rate of the USART peripherial without
+*		 : re-initialising.
+* Input          : USART to change, new baud rate
+* Output         : None
+* Return         : None
+*******************************************************************************/
 void UARTChangeBaud(USART_TypeDef* USARTx, uint32_t Baud)
 {
 	/* USART BRR Configuration */
@@ -171,6 +214,7 @@ void UARTChangeBaud(USART_TypeDef* USARTx, uint32_t Baud)
 	USARTx->BRR = (uint16_t)tmpreg;
 }
 
+
 /*----------------------------------------------------------------------------------*/
 /* WORK IN PROGRESS BELOW */
 /*----------------------------------------------------------------------------------*/
diff --git a/flight/sys/pios_uart.h b/flight/sys/pios_uart.h
index 0fb1bfe09..e6a30232d 100644
--- a/flight/sys/pios_uart.h
+++ b/flight/sys/pios_uart.h
@@ -28,7 +28,7 @@
 #ifndef PIOS_UART_H
 #define PIOS_UART_H
 
-/* Function Prototypes */
+/* Public Functions */
 extern void UARTInit(void);
 extern void EnableAuxUART(void);
 extern void DisableAuxUART(void);