Hi yes I have done this for some games (using moonlight 2.0.1) but I er didn’t have to do anything once I had moonlight running. I added moonlight to emulationstation with the command to pair with my PC and then to run against Steam. The controllers ‘just worked’ for any game that didn’t have a crap xbox mapping file (e.g. Towerfall Ascension doesn’t work unless you change the mapping, which I haven’t gotten around to doing yet). Games like dungeon defenders worked with at least 2 player though using 1 wired xbox controller and 1 wireless xbox controller.
What part are you having trouble with / what game are you trying to play?