So once you get your program working perfectly on your development board (say.. AT91SAM7X-EK), what is the next step for adapting it to the actual device you are trying to build (say.. using the AT91SAM7XC128)
If using different chips on development board and real target (unless the chips are just about identical), then I would not wait for the program to work perfectly on the development board. I would jump a lot quicker to real hardware, to get more hands-on time there.
And I would normally not jump in with a full program when activating new hardware. Normally, I test with smaller applications intended to verify different parts of the hardware. When the hw seems ok, and any important differences between development board and real hardware has been handled, then I activate block after block of the real application.