ok, so xboxdrv_mapping.cfg is what is used by the xbox drivers to map the buttons and joysticks on your xbox controller to keystrokes and whatnot.
the piplay controller config asks you to configure your buttons, then directly re-writes the configuration file for that emulator. It is just a convenience thing. You can manually rewrite the snes9x.cfg file yourself if you want to. It's the same either way.