Yeah man, I make my own and it was an expensive learning process. When I first started I was using a regular 1 1/8 inch hole saw bit on a drill, I kept cracking the plexi glass, sometimes on like the very last button, it was so frustrating. The part that was actually cracking the plexi glass was the drill bit part of the hole saw, once that got through I'd use the drill high speed and the hole saw part would go through smooth. So the solution, I use a dremel with this plastic cutting bit high speed and put one little hole in the center of where each button goes so the drill bit part of the hole saw doesn't ever make contact with the plexi glass. This is all being done with the plexi glass clamped to the control panel with buttons already drilled out of it.
As far as cutting the plexi glass to fit your control panel, here's a valuable lesson, DO NOT have some idiot at Lowes or Home Depot do it for you, they can only get within like 1/4 inch or so of the dimensions you specify, if you go this route, tell them to cut it a quarter inch or so larger than the size you actually need, then clamp the plexi to your control panel and use a palm sander (this works great) on the sides to get it to perfection.
I also use a dremel to cut the pexi glass close to the size I need then sand the edges to perfection, its a high speed plastic cutting bit, the cuts are super clean. I got the dremel on sale for like $40 and I also use it for t-molding and doing the inlay to mount the joystick with a router attachment. The bits are what cost all the money though, that's where they get you.