Unfortunately, I do not have an XBox controller, so I do not have any experience with setting up xboxdrv. However, there is an an article about that in the wiki. Also, every input device that represents itself as a gamepad/joystick to the OS can be configured wo work with RetroArch and the other emulators that can be installed with the RetroPie Script. Also for that issue exists an article in the wiki.
Currently, NXEngine cannot be installed by the RetroPie Script. There are ports of NXEngine for the Raspberry, however, and if you know of a reliably and satisying working version, I would be glad if you point me into that direction :-) It would even be better, if you could come up with a pull request for the RetroPie Script at https://github.com/retropie/RetroPie-Setup ;-)