I have used quite a few IDEs both commercial and free. My favorite is IAR - for its simplicity and utilitarian approach.
I have used Eclipse, and found it to be quite good. However, for avrs, my favorite free IDE is Code::Blocks. It is very simple, small, and runs fast. Give it a try and you may like it.
AS5/6 are not bad but too big, especially with AS6.
You may also try Source Insight - excellent in my view but pricy. Programmer's Notepad is free and a better tradeoff between functionality and price.
As to code orgnization, I organize my code into .h and .c files and simply copy them to the projector folder, in the development phase.