Not saying anyone's ideas are all wrong. Lemme see if I have you correct first, and I'll reply based on my assumption of what you want. I use templates for doors, handles, hinges...all kindsa stuff on a daily basis (I do remodels in wintertime - kitchens mainly)
You want to use your template to tell you where to drill the holes on your CP. That's my understanding of what you are looking to do.
Set up your templates on your CP. Take an awl (screwdriver looking thing with just a sharp point on it) or some other such implement (a nail works too) and punch the center of each button/joystick hole - right through the paper, and hard, to give you the mark of where to drill on the CP. When done, remove your templates, and drill, using your template as an idea of where to look for your marks in case you didn't press hard enough.
If you don't have "cross-hairs" on your buttons or joystick holes, go into Photoshop and make 'em. Just add a layer, add a shape (line), and place them into your image until you get a "+" on your button/joystick holes.
If you are trying to freehand the holes and don't have crosshairs on the hole area, good luck. The crosshairs are vital to getting your alignment correct. Each bit you are going to use (forstner, spade, holesaw, drill) to drill the holes ALL have a point in the center to help you center the hole. Use the Photoshop crosshairs to help you better use the hole bit.