To get controls to work we need to bring up the Retro-Arch RGUI menu.
On this page:
https://retropie.org.uk/docs/Atari-800-and-5200/
If you are using lr-atari800 you will want to set the controller type to “Atari Joystick” and not “RetroPad” in order to get all the keys mapped to your controller.
This setting is in the Retro-Arch RGUI menu NOT the Atari Menu.
Press Select + Start to get into RetroArch -RGUI.
Press F1 on Keyboard to get into lr-atari800 config menu.
To make the lr-atari800 work with a Joystick you will want to make a Core Remap override to preserve the use of “Atari Joystick”.