I usually do what you mentioned. I poke small holes and line it up that way.
If the holes in the CPO haven't already been drilled then I use clamps to hold down the cpo and then use a whack of an 1/8" punch in the center of each joystick or button space to use as a drill guide in the wood.
If the holes are drilled already then I try to clamp the art where it should go and then slightly press on the surface to make sure the holes look lined up, hold it up to the light, etc. When I'm pretty sure it's lined up, I flip the cpo, use a drill/spade bit the size of the hole, lined up in the hole to create a tiny pinprick in the cpo buttons and joystick holes, dead in the center of each. Then I flip it over to make sure it looks dead center still, and make adjustments from there.
Oh and a few tips: use a plastic bondo scraper or vinyl applier, working from the center out to get out air bubbles. Work slowly. If there is an air bubble you absolutely can't clear, use an exact with a fresh blade to pop the air bubble by making a very small cut. Long term you won't notice the tiny cut vs an air bubble. If you have to wrap around edges, triangle cut at the edges of the panel so that there won't be a lot of material overlap. Finally, I usually use a few staples or tacks on the back to keep the cpo firmly in place while the glue sets and so that the stuff never peels up in the future.