I wrote several articles for Nuts&Volts about this topic, Smiley's Workshop 10, 11, 12 that can be gotten off my website www.smileymicros.com.
I kind of hesitate to recommend them though since one of the things I learned writing about this was that I found myself using the Arduino IDE exclusively for what Arduino is good at, and using AVRStudio for the things Arduino wasn't designed to do.
I've seen a lot of folks that seem to want it both ways, that is to make Arduino do everything the 'real' tools do and/or make the 'real' tools as easy to use as the Arduino. Frankly, the more I look at this concept, the less sense it makes.
Arduino is great for designers , newbies, hobbyists, etc. and even raggedy old engineers like me who just want to do a quick test of something simple. But for things it doesn't do easily, it just seems strange to try to bend it all out of shape and get folks all confused, when one could just switch over to AVRStudio/WinAVR/AVRDude.
Maybe I'm missing something.
Smiley