Try sudo nano /RetroPie/configs/all/retroarch.cfg (not actually sure this path is just right off the top of my head). You can also open it up in x by typing “startx” and opening the file manager.

Scroll to the bottom. Look for input_player1_joypad_index = “0″ Copy everything beneath it and paste it. In the copied set, change all instances of “player1” to “player2,” set “joypad_index = “1,” and put in the correct values for this controller!

Hope this helps!