I've got it figured out. I mapped the buttons as if I had an SNES controller (backwards). This corrected the problem with SEGA. The only issue now is that in EmulationStation, it says to press A to enter, B to go back, etc. For somebody not familiar with the system, that can be confusing. By going through the RetroArch-Setup scripts and swapping the A/B buttons, it only does it in EmulationStation. So everything now works like it's supposed to.
Thanks! On to my next big project!