Which system are you referring to? Emulation usually involves configuration files either global or per title eg Amiga Forever where in editing the RP9 file with right button menu you can select the INPUT menu and choose Gamepad over None or Joystick. Interestingly in that case a PC Xbox controller will work with Gamepad set but not Joystick.
According to Google, An A500 mini can run external adf's if the firmware is updated to v1.1.1. To run the game, start the game with the supplied gamepad then press HOME + X to swap control to a joystick.