You may not be able to use the Xbox One controller because I’m not sure it’s supported by xboxdrv yet. You could use and xbox 360 controller though. Either way, you want to install xboxdrv, which you can do from the retropie_setup.sh script under option 3 (i believe). Make sure you restart after installing xboxdrv, then go back into the setup script and walk through registering a retroarch controller.
After that, you’ll be about 85% set up as retroarch doesn’t cover all of the emulators.