Doing what you suggested but adding .atr/.ATR as well as the others did mean the atari option now shows up on my main screen, and lists all my roms. It didn’t unfortunately create the atari800.cfg anywhere on the Pi, I’ve ran a full search of all of it and it’s just not there. Not sure if this is again something to do with the extensions or another issue.
I’ve had a look at what you posted for the Rasbian version, it does look quite tidy but i’m trying to integrate this in to Emulation Station as it’s for someone very untechnical and i’m not sure if I can do that. I’ll have a read around though and see if/how that can be done.
Feels like i’m very close now to getting the built in version working on my retropie but I must still be missing something :(
Thanks for your help. I’ll post back if I am able to find any other way to get this going.