If you intend in using a multi-button joypad or joystick that is compatible with the MorphOS lowlevel.device (which only includes USB and the Pegasos PC-style joystick port as far as I know - I never owned a Mac!), the lowlevel functions are:

JPF_BUTTON_BLUE Blue - Stop
JPF_BUTTON_RED Red - Select
JPF_BUTTON_YELLOW Yellow - Repeat
JPF_BUTTON_GREEN Green - Shuffle
JPF_BUTTON_FORWARD Charcoal - Forward
JPF_BUTTON_REVERSE Charcoal - Reverse
JPF_BUTTON_PLAY Grey - Play/Pause
JPF_JOY_UP Up
JPF_JOY_DOWN Down
JPF_JOY_LEFT Left
JPF_JOY_RIGHT Right

Maybe you can map these as keys in the E-UAE config (maybe without the JPF_ part). Maybe you don't even have to and E-UAE will take care of it.

The MorphOS port of E-UAE, if it even supports joysticks at all, must use lowlevel.library
- or have Poseidon map USB functions to keys. MorphOS has no other way of controlling joysticks as the original Amiga hardware-banging doesn't work.