Self-answering...the solution, of course, is to turn on focus mode, something I'd never heard of before today. Live and learn. :)

@dch It seems you're using an older RetroPie version and from what I see in the Docs, UAE4ALL doesn't seems to properly support joysticks.
Try to update to a more recent RetroPie version and use Amiberry. If your gamepad works in other games/systems, Amiberry should be able to read the configuration created by RetroPie and use your gamepad.

YAY! got it working thanks to https://retropie.org.uk/forum/topic/18409/guide-getting-emulationstation-to-work-with-fs-uae

Had to install fs-uae manually first because of the gpg error then try to install with retropie-setup then follow the step above

All you guys rock :)

Time to go shoot some guys in Walker

@cacrlhungus74 This is old and maybe you already resolved, but i found saving config file under Amiberry you could also save game-specific controller mapping.
Althought i can only achieved mapping some keyboards commands (like F1) on controller shoulder buttons, which seems reasonable considered frontal buttons are needed for Cd32 games.

@SpudsMcToole I’m new to Amiga emulation... Have been trying this but it doesn’t load as seems unable to load the right rom

@spudsmctoole It did :)

@SpudsMcToole
didnot work for me