Good call. I checked there and there is no simple config as of yet. Here is what that forum said:
KEYS: ~~~~~ These are the default keys. You can't reassign them without a recompile at the moment, sorry about that.
SNES A: D SNES B: C SNES X: S SNES Y: X SNES L: A SNES R: F SNES Start: Return SNES Select: Tab SNES D-pad: Arrow keys Turbo: Backspace Quit: Escape
If you want to change the keys you need to edit unix/keys.h and then re- compile. Please see http://www.libsdl.org/cgi/docwiki.cgi/SDLKey for a list of key symbols you may use.
I found there is a better way to do this now. There is a config file snes9x.cfg at /home/pi/emulators/pisnes. I mapped in the A, B, X and Y buttons. Here is a snippet from my config file.
[Keyboard] # Get codes from /usr/include/SDL/SDL_keysym.h