AVRStudio 4 was pretty slick but I was forced to move to AVRStudio 5 to use the 4313. It's based on .net so it is slow and clunkey and initially rather buggy. But it got better.
I've done some development under Linux using Eclipse and AVRDude but the Windows/AVRStudio path is probably easier, and if you are using a Dragon for debugging Windows is much easier. Love me some penguin though. Do nothing on Windows but AVR anymore.
It was a real mistake not to make studio5 a cross platform IDE.
Atmel needs to support Win/Lin/Mac
I still mostly use studio4.