Essentially what I did was the following:
I went into the files appdata/local/visualGDB/EmbeddedBSPs/at91sam7s-ek folder, and created a replicate of the flash.lds file. I renamed both files bootloader.lds and code.lds respectively. I then edited the SRAM/FLASH memory allocation for both to match the memory allocation on the .map file generated by the .xcl in the original IAR code I am converting to VS.
After building the solution, I select the Debug/Program and Start Debugging option, It seems to only be loading the bootloader.elf file into the MCU. I confirmed this when I selected the Debug/Start without debugging option. Essentially despite the fact that I have two .elf files in the solution( the bootloader.elf and the code.elf file) , its only programming the bootloader.elf.
What I did is that I created two new solutions a solution simply for the bootloader code, and a solution for the code. I also changed the .mak file in these solutions to read the booloader.lds and code.lds respectively. I then programmed the solutions one after the other and the behaviour of the MCU was consistent with how it would behave had I programmed it with IAR.
Essentially I am trying to create one solution with two project whereby one .elf file is programmed and is followed by the second one. Is there anyway to two this with VisualGDB?