Quick Reference:Â
Load a rom | Press Select and Y | Main Menu | Settings | Onscreen Display | Onscreen Overlay | Change Display Overlay from ‘ON’ to ‘OFF’ | go back to the Main Menu | Quick Menu | Save Core Ovverides | Reboot Pi (may not be required)

A Little More Detail:
Select a system then load a game, after the rom loads press Select and Y, the Main Menu will now appear. Scroll down to Settings, then select Onscreen Display, then Onscreen Overlay, change the Display Overlay option from ‘ON’ to ‘OFF’. Go back to the first page of the Main Menu, scroll to the top and select Quick Menu; at the bottom of the Quick Menu you can Save Game Overrides, which will save the bezel changes for the game, or Save Core Overrides, which will save the settings changed for the system.

This did work for me for some systems, but not for all. When I made the changes for the NES some games lost the bezels but some did not. MAME wouldn’t save to Core at all, I would have had to go into each individual rom and Save Game Overrides.

If anyone knows of another way, please feel free to share!