I don't know about that particular emulator, but you may need to turn on joystick support. For example, in MAME, it's joypad=1.
Alternatively, you can get a remapper, such as joy2key or XPadder to take care of this for you. These programs convert joystick buttons to keyboard presses, which is great if your emulator doesn't support gamepads at all, such as NullDC.