If you are using the default SNES emulator (pocketsnes) it has issues with two player- at least in my case. Only the 1 player controls worked even though my second controller has been registered and is working in other games. If you have a Rpi2 then you can install the snes9x next experimental package from the setup script and it worked fine for me after that. See this video (at about 7 min) on how to do that:
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