Gratuitous description of problems encountered
So I was originally running crunchbang (debian based OS) and arduino 0018 (the version in the repository). I went through the installation steps at http://sanguino.cc/softwareforlinux. I did not running the debian specific steps because I checked my versions and they were much greater than the ones listed in the how to. The sanguino options appeared in the arduino software and I picked the 644P option which I confirmed on the hardware. The issue came when I went to upload a sketch. I would try the blink sketch but I would always receive the message of
From here I panicked that I did something foolish during hardware assembly and triple checked everything. Once I was fairly sure that was fine I tried the ubuntu specific steps from the previous sanguino link. That also did not work. I tried a ton of other steps like manually resetting before uploads and updating to 0023 and 1.0 from the arduino site, repeating steps for each of those versions with no luck. With arduino 1.0, no sketches would even compile.stk500_recv() programmer is not responding
So then because it was going to happen eventually for unrelated reasons, I reluctantly switched the computer I was on over to Ubuntu 12.04. I know don't think this helped or hurt, but I am adding it for completeness. I then installed arduino 1.0 from the repository and had the same issues as with crunchbang and 1.0. I also tried 0023 from the arduino site and sketches would compile but I would still get the not responding error from above. I tried a pretty much everything I did with crunchbang along with trying some different sources for the sanguino software, none of which worked until...
Solution
I tried using the software from https://github.com/whirleyes/mighty-1284p and it worked like a charm. Just put the files in a folder just like you would with the sanguino software instructions. This allowed me to compile and upload to a sanguino with the arduino 1.0 software. I was kind of avoiding the 1.0 software for a while because it seems like there are some significant changes, but in the back of my head, once I maxed out the room of a BBB, I knew it would be best to make the 1.0 changes now rather than later.
I hope this helps, and please if you have anything to add or if you feel that I did something wrong, let me know.