If you are using AS6 the ICE is the way to go, it is very fast and works well in the 328 debugging I've done.
I also made a 100mil adapter board for it to get away from those 50mil connectors:
Thanks for the great design!
And here is my contribution for those who buy the Atmel ICE debugger in the bare PCB form:
Have designed an enclosure for printing on 3D printer.
You can find it published on thingiverse.com at this address:
http://www.thingiverse.com/thing:983293
Your case turned out great funycat!