Lovely game! I can't seem to find a way to map the fire button to my gamepad... It looks like the x key is hard coded?
On a gamepad the confirm button ("A" on XBOX360), as well as both triggers and both bumpers should all work as fire buttons. It's also possible you might need to use the downloaded version of the game to get it to recognize your controller, I know I've had some trouble with that in the past.