Sorry, I only checked if 2600 worked for me, but did no further configuration yet, because my priority was C64 and Amiga.
Did you check the wiki? https://github.com/RetroPie/RetroPie-Setup/wiki/Atari-2600
“Press Tab to access configuration menu- choose input settings and under the tab Emul. Events you can create custom controller mappings to work for your individual controllers”
