missed the sudo commands..
at the bottom on the /RetroPie/configs/all/retroarch.cfg file, you will see input_player1_joypad_index stuff, delete all of that…
then drop into terminal (F4) or ssh and do this..
sudo ./retroarch-joyconfig -o p1.cfg -p 1 -j 0
( -o for output file, -p for player, -j for joystick id )
then do this
sudo cat p*.cfg >> ~/RetroPie/configs/all/retroarch.cfg
this will setup the controls for the emulators, if you need to do the emulationstation controls, delete the esconfig file in the .emulationstation folder and reboot.