For what it’s worth, I’d recommend grabbing the fsm branch instead of trunk. I do most of my development in the branch, and merge it into trunk every few weeks after a round of more detailed testing, so trunk is generally a few weeks behind.
I’m not sure how the build works in Atmel Studio. I mostly just run ‘make’ from a command line, to compile all the supported build targets. Each cfg-*.h file is a build target. I’m guessing Atmel Studio will need some settings copied from the bin/build.sh script into the GUI somewhere, to set up compiler options and include paths.
For an introduction to FSM and how to use it, I’d suggest looking at the first few posts of the FSM thread, or at the Baton UI code which is intended to demonstrate the general pattern. There’s also some documentation which may be of use, though I don’t always remember to update it when the API changes. I find it easier to learn by example than by reading documentation.