Oh I can only imagine you meant my "oops"
Do you freehand it, or do you have a stencil? Also, what bit are you using in the router, and do you countersink with it too??? I think you mentioned it to me before, but I'm just scared of that damn thing I think. I always seemt to try and find alternatives to using it
However, after that last screw up, and the time it took me to re-drill, sheesh, how much worse can it be? 
(off to try the router in some scrap plexi)
Yes, I was referring to your "oops".

Using the below pic as an example, I'll try to explain exactly how I do mine:

First I drill out the control panel wood with a spade bit, or use a router w/ circle jig to make all the holes for buttons, joysticks, spinner, etc. Then I cut a piece of plexi slightly larger than the wood cp. I locate the spots for the screws, and then use a c'sink bit (reference
www.mcmaster.com part number 3013A112) with a drill press or hand drill. BTW, I was wrong in my previous post, my c'sink bit is a 3-flute not single flute.
Now I screw down the plexi to the wood control panel so it is secure. Flip the control panel over so the plexi is on the bottom and start routering the plexi since the wood cp is now the template for the plexi. This is the router bit I use for cutting plexi:
http://www.leevalley.com/wood/page.asp?page=30166. Template router bits like this have a bearing at the top, unlike laminate trimming bits with the bearing on the bottom. I personally like template bits much better than laminate bits exactly because you can plunge with them into your work rather than drilling large pilot holes. Then I buzz around all the edges and inside the holes with the router and now the plexi is a perfect match for the control panel.
It probably took me almost as long to write this as it would have to actually make the plexi overlay this way.

It seriously is a very quick, easy, and super accurate way to make plexi overlays without risking cracking them. Once you start using your router for things like this, you will wonder why you weren't doing it this way all along. My router is my most valuable tool and I constantly look for ways to take avantage of using it in projects.