The .atari800.cfg file is located at /home/pi
Just to confirm, the raspbian version of atari800 should get copied to:
/opt/retropie/emulators/atari800-3.0.0/installdir/bin
Make sure the ownership of atari800 is 7777.
I am not familiar with ATR extensions. Are those Atari 800 system files? I am using it to run 5200 games.
