Batocera provides two different ROMs directories for Amiga:

• /userdata/roms/amiga500: home for all Amiga 500/600 “OCS/ECS” games
• /userdata/roms/amiga1200: this is where you put “AGA”-only games.

AGA and OCS/ECS Amiga architectures are quite different, but in a nutshell and with some exceptions, AGA games are usually visually much more attractive because they can render a palette of 256 colors on the screen with bigger sprites, while OCS/ECS are limited to palettes of 32 colors.