Programming

Programming the Make Controller when using the Prototyping Board is slightly different than when using the Application Board.  If you haven't already, you'll want to familiarize yourself with the Make Controller firmware API, which can be found here.  You'll also want to download the appropriate toolchain to compile the firmware, and mchelper (Make Controller Helper), an application that will allow you to upload your new firmware to the board - check the Downloads Page.

General Purpose IO

One particularly useful library when using the Prototyping Board is the IO system. There are 64 general IO lines on the SAM7X, broken into two banks of 32.  Each can be an input or output and, confusingly, some lines can be used for up to three different peripherals.  The IO system makes it easy to control these lines, and provides a way to lock lines that you only want to be used for a single purpose.

Note, however, that not all of the 64 GPIOs are available to you on the Make Controller.  Some of them are tied up to things like the Ethernet PHY and the CAN transceiver.  Consult the Make Controller Pinout for a diagram of which pads correspond to which IO lines on the Controller.

Controller Specific Modules

Since your Prototyping Board project won't use the Application Board, that means you cannot (without some effort) use the AppBoard firmware module.  You'll only be able to use the Controller Board section of the API.  If you develop modules for other pieces of hardware, please consider sharing them in the Extensions section.