Khoth, I haven't encountered a VCS that will handle resource forks out of the box. You could probably do some AppleDouble magic using commit hooks, but that's a pain. The first thing I did with the source was to move all the resources to the data fork by running "DeRez foo.rsrc > foo.rez && Rez foo.rez -o foo.rsrc -useDF" for each resource file. As I mentioned above, this is the Apple-recommended way to store them these days, since it helps apps to not get destroyed by zip.
I've made an XCode project that will build all three BoE apps (once carbonisation is complete). I've been doing some carbonising, starting with the character editor because it looks the easiest. I wouldn't want us to be duplicating effort, so maybe we should try to coordinate, and share a source repository?