I fixed it!
ok…what I did was manually added the player 2 configuration in the retroarch.cfg file. I’m sorry I can’t give you everything I did because my Pi isn’t hooked up to anything at the moment. So this isn’t exactly what I have but it’s pretty close.
input_player2_up = u
input_player2_down = d
input_player2_left = l
input_player2_right = r
…and so on for all the buttons. worked like a charm!
Now I just have to get my track ball to work and I’m all good.