Supern64 (based on mupen64) allowed my right stick to map to the c stick properly, at least it was registering as the c stick in the device setup in that emulator, I didn't get far enough in majoras mask to actually test it in game but it seems like it will work and blocks the mouse from displaying.
The snes emulator I tried didn't but I don't need the right stick for snes.
That said those other two apps the wrc1010 listed have worked for me in the past along with bluezIME. Those two apps are really cool for mapping touch controls to physical buttons as well. We just need to have a rooted device for that function.