if your talking about setting up a wireless xbox 360 cotroller, do this—i setup mine this way and it works both on emulationstation and emulators..just go into terminal and type…
Sudo chmod +rw /opt/retropie/configs/all
Cd /opt/retropie/emulators/RetroArch/installdir/bin
./retroarch-joyconfig –o /opt/retropie/configs/all/p1.cfg –p 1 –j 0
Follow directions
Sudo reboot
hope that helps..let me know