I normally use WinAVR for my AVR related projects, but recently found the need to use Atmel Studio. The problem is, I use a USBasp to program my chips, but Studio does not support that particular programmer because it doesn’t follow Atmel’s protocol.
Anyhow, the easiest solution I found was to write the code in Studio, compile it in there, and switch to my command prompt in order to burn the hex file using avrdude. Personally, I found that to be easiest way. You could probably set up an external tool in Studio if you want, but this works just as well.
Just wanted to document this for myself as I see myself stumbling into this problem sometime in the future again, and for anyone else looking for a quick solution.