First, are you on 3.0 beta 2? because if not, you should update to it.
Second, you should update your setup script, and install the testing emulators if you are going to run n64 games. I have found the mupen64+ testing glesN64 works well with mario themed games except Yoshi’s Island.
Third, if your controller is listed in the /n64/InputAuto.cfg file, it should work for you.