Where should a bootloader code be written for a microcontroller ?

See more:

embedded

C

Flash

I am developing a boot loader for first time for a kinetis controller in Kinetis Design Studio (IDE). Since the Boot loader should be the first code to be executed, should I create a separate source file (say BootLoader.C) apart from the automatically generated Main.c file by IDE. Or should I write it in the Main.c file itself?
THIS IS HOW THE MAIN.C LOOKS LIKE.. WHERE SHOULD I PLACE MY CODE

Filename    : main.c
**     Project     : TestBeta
**     Processor   : MKE02Z64VLD2
**     Version     : Driver 01.01
**     Compiler    : GNU C Compiler
**     Date/Time   : 2016-02-12, 11:47, # CodeGen: 0
**     Abstract    :
**         Main module.
**         This module contains user's application code.
**     Settings    :
**     Contents    :
**         No public methods
**
** ###################################################################*/
/*!
** @file main.c
** @version 01.01
** @brief
**         Main module.
**         This module contains user's application code.
*/         
/*!
**  @addtogroup main_module main module documentation
**  @{
*/         
/* MODULE main */


/* Including needed modules to compile this module/procedure */
#include "Cpu.h"
#include "Events.h"
#include "Bit1.h"
#include "BitIoLdd1.h"
/* Including shared modules, which are used for whole project */
#include "PE_Types.h"
#include "PE_Error.h"
#include "PE_Const.h"
#include "IO_Map.h"
/* User includes (#include below this line is not maintained by Processor Expert) */
SHOULD I WRITE THE BOOTLOADER CODE HERE ?????
/*lint -save  -e970 Disable MISRA rule (6.3) checking. */
int main(void)
/*lint -restore Enable MISRA rule (6.3) checking. */
{
  /* Write your local variable definition here */

  /*** Processor Expert internal initialization. DON'T REMOVE THIS CODE!!! ***/
  PE_low_level_init();
  /*** End of Processor Expert internal initialization.                    ***/

  /* Write your code here */
  /* For example: for(;;) { } */
SHOULD I WRITE THE BOOTLOADER CODE HERE ?????
  /*** Don't write any code pass this line, or it will be deleted during code generation. ***/
  /*** RTOS startup code. Macro PEX_RTOS_START is defined by the RTOS component. DON'T MODIFY THIS CODE!!! ***/
  #ifdef PEX_RTOS_START
    PEX_RTOS_START();                  /* Startup of the selected RTOS. Macro is defined by the RTOS component. */
  #endif
  /*** End of RTOS startup code.  ***/
  /*** Processor Expert end of main routine. DON'T MODIFY THIS CODE!!! ***/
  for(;;){}
  /*** Processor Expert end of main routine. DON'T WRITE CODE BELOW!!! ***/
} /*** End of main routine. DO NOT MODIFY THIS TEXT!!! ***/

/* END main */
/*!
** @}
*/

What I have tried:

I am trying to write the code right after the header files. I have included other required header files which is followed by the snippets of code.. I didn't execute and see yet. Which is the correct method