Ok, I’ve gotten Player1 to work. I can use it inside ES as well as a game. I used this (just like 500 times before) and it worked this time, oddly.
sudo chown pi /opt/retropie/configs/all/retroarch.cfg
cd /opt/retropie/emulators/RetroArch/installdir/bin
sudo ./retroarch-joyconfig -j 0 >> /opt/retropie/configs/all/retroarch.cfg
However, when I go to the retroarch.cfg in the GUI to edit and add values for player 2 the values for player 1 are blank. My goal is to get both gamepads working within the ROM, but if I cant edit the cfg how am I supposed to do that.