It's so cool seeing how people are remixing GemSet! I knew that including the default color scheme and a default-ish tileset would encourage people to give their game a custom look.
Max, what you're doing sounds about right. I currently have Python 3.4.2 installed (for PyGame) and the following changes in my run.config:
source=resources/gemset
target=resources/vanilla
output=resources/output
If you put the BAMM! files in the source folder and your raws in the target folder, it should work. I haven't tried anything other than vanilla raws, though, which might be the source of your problem.