Since finding this site, I have setup a laptop dedicated to robotics. Over the weeekend, I decided to put Linux on it as a dual boot. I have read that it is difficult to setup a Linux machine to do AVR programming and I wanted to find out for myself. It has actually gone really well, and has been alot easier than I could have anticipated. I plan to write up a tutorial on it in order to help anyone else wanting to do the same.
More to the point of the post though, I currently have both C and C++ code compiling for AVR in Linux. I am currently working on the programming of the chip now, both the ATmega8 and the ATmega640. I am using the AVRISP mkII programmer and will be using AVRDUDE to write to the chip. Does anyone have experience using AVRDUDE that could save me some time in reading all the documentation?