dhenry:
If so, what do I need to do so that it can accept AVR code?
I would get a standalone programmer. They are so cheap now and provide you with the flexibility to move up to a new world without arduino.
I really would like to get a standalone programmer but my budget is a bit tight (college student studying electronics :P) and since I already have an arduino I thought I might as well use it. I searched through the forums a bit more today and found this thread: Arduino Uno R3 as a true ISP programmer for any AVR - #21 by simplex - Microcontrollers - Arduino Forum which I think is similar. The guy who started the thread mentions that his Atmega chip has an arduino bootloader. So I think I should be fine if I follow that procedure. (Hopefully)