Yeah, I actually ended up finding it after I posted this. Sadly, it doesn't look like you can get 2U saves to work though. Even swapping out Cxbx's EEPROM.bin file with the one from your Xbox doesn't work.
EDIT: Importing a 3.1 save didn't work either. Hmm.
With the latest version of CXBX, the UI works now (though only in windowed mode atm) Also modding has also got a LOT more easier. You can simply drag costumes over to the emulator's Partition save folder.