To program the AVRPi boards, there are a couple of libraries and tools you can use. Most of the software described below have their own page, but here's the short version:
The IDE you probably already know, and may or may not hate. However you feel, the Arduino library itself is still useful.
Use the Arduino library with your favourite text-editor/IDE.
If you're serious about creating a USB device out of the AVRPi-32u4, LUFA is the way to go.