Well, I have solved my own problem but I’m not sure if I can help with yours. After I posted this, I took a short break from trying to get it to work before starting over. I installed an updated version of RetroPie via the SD card image rather than setup script. I had read that the newer version supported transferring EmulationStation’s button mapping to RetroArch, which was in fact the case. Now, if I map a contoller in EmulationStation it automatically maps it for RetroArch which solved my problem.
In short, using updated SD card image fixed my problem.