I haven’t played with that particular emulator, but if you’re having control issues, take a look at the xboxdrv documentation. There are some really handy features for the controller. (IMO the xbox 360 controller is hands down the best controller for the pi.) In particular, look into creating some extra config files and the --next-config option. The default behaviour of the xbox button is to change controller modes. I use this to be able to control atari 5200, 800, and ST, as well as c64 and Amiga. If you want more details I can provide some of my controller config files, and what you need to modify in rc.local to get that working.