Hi Psyberbob,
i do not have this board, but the things to get a led on/ off, which is connected to a gpio pin, is basicly the same for all controllers.
1. set the direction
2. set/ clear the pins (some controllers have one register for setting/ clearing, some controllers have separate registers for setting and clearing)
The source code you mean (i think) includes all the the things to power on the system (interrupt table, memory initializing and preparing the C-startup). This can be very different between the controllers. Atmel startet at very low frequency, which is a good solution for saving power. But you have to do more at startup (setting the frequency to higher values).
After the startup is done, you can control the led like described above. Note that the AT91 chips use one register the clear (level zero) and an other register to set the output. In a third register you can sample the actual status.
I suggest start programming, using the debugger (mostly Angel) inside. To connect it, you need the ARM SDK (it is quite extensiv but there is a 30 day demo version available) or the GNU debugger. The last one is free.
Write your programm, link it for the ram area, transfer it to the platform and run it.
Best regards,
Edi