If you plug your controller in before starting the game then it should automatically be setup.
If you made changes though then they might be saved and you will have to reconfigure.
Press tab.
Select "Input (this Game)"
Change "Lightgun X Analog". Press left or right.
Change "Lightgun Y Analog". Press up or down.
For me the controller was way too sensitive.
To make the game challenging you do not fire directly at the cross-hairs. The farther from the center of the screen you are the farther from the cross-hair you will hit. Practice when entering you initials and watch for the blast from your gun, that is where you are actually hitting. This game is very difficult to do with just one quarter. You would be good if you get to the gate your first time.
---------- Post added at 05:18 PM ---------- Previous post was at 05:13 PM ----------
To make the controller a little less sensitive and easier to use or if you just do not have a digital controller then do this.
If you Change "Lightgun X Analog" and "Lightgun Y Analog" both to none by pressing enter and then escape. And then
Change "Lightgun X Analog Dec" to left.
Change "Lightgun X Analog Inc" to right.
Change "Lightgun Y Analog Dec" to up.
Change "Lightgun Y Analog Inc" to down.