For mame4all press [Tab] wenn you are ingame. There you can configure the controls for mame4all and the different roms. It may be possible that saving won’t work since mame wants to write the config files to /opt/retropie/emulators/mame4all-pi/cfgs which needs root privileges. If that’s the case you have to run mame manually with sudo and configure the controls.

pifba has it’s config file in /opt/retropie/emulators/pifba and it’s called pifba2x.cfg I think. You have to configure your controls manually in the file.