The thread is kind of old, but this may be still be of interest to some... I had the same problem, but after fiddling around in the settings I eventually managed to come up with a solution (under WinUAE 3.2.2):
In the configuration of my Joypad under Host->Input I set Button 1 to "Joy2 Fire/Mouse2 Left Button" with autofire/toggle, and additionally Button 4 to "Joy 2 Fire/Mouse2 Left Button" without autofire (see attached picture). Thus I can use autofire by keeping Button 1 pressed and deactivate it by releasing the button. Moreover I can also use the surround flash by keeping Button 4 pressed. No need to go into WinUAE's menu during the game.
