I've not used any controller device with my atari800 emulator. I figured the actions are just left, right, up, down, and fire, and that the keyboard would suffice. I use a desktop keyboard with separate number keys, so it made sense to just use those keys plus another for fire.
I notice there is a man page for atari800. You may find something useful in this:
https://manpages.ubuntu.com/manpages...tari800.1.html
or just type
man atari800 in the terminal. This may get you a newer version as well.
I've managed to get by with the F1 configuration dialog, although using it can be very frustrating.
If you ever venture outside of Ubuntu Land, version 5.0.0 of atari800 is now offered by Fedora, Arch, Manjaro and possibly other Linux distros I am not aware of. I have the 5.0.0 version on Fedora and it works well. And it's not a snap package.