I actually just got done drilling my CP and lexan. A few tips:
1. Be sure to remove the lexan circle from the drill bit after each hole. If you don't, they'll start to accumulate in the bottom of the bit and burn together, in which case it's a real pain in the ass to get out, and the length of the bit shortens substantially so you end up burning everything.
2. My bit wasn't quite long enough to even make it through the lexan and wood with out burning the hell out of the middle of the wood. To fix that, I just flipped the ensemble over after I was done and drilled from the other side. It was quicker and easier and burnt the wood a lot less.
3. Don't drill both CPs at once. Honestly, if you go that route and you mess up, you've essentially just ruined the point of having a back up CP, and you'll need to buy two new ones. Not good.
4. Don't put too much pressure (hardly any) on the drill when you're going through the lexan. It might crack, or it might slip and scratch the hell out of the surface. Either way, it only takes about ten seconds for it to make it through, assuming you have a sharp bit. Just hold it on top of the glass and you should feel it give way.
5. I put the paper under the lexan. While it might give additional protection, if you wind up slipping and skidding across the paper, the amount of protection it might offer probably wouldn't be enough to stop a skidding, running drill. Plus, if it's on top, there's a higher chance of it tearing (at least I would assume) than if it were clipped underneath the lexan and sandwiched there.
Like I said though, I'd drill the two CPs separately. Just use the first CP as a template for your second, or use a second sheet of paper if the first gets torn too badly. You could even use a fairly long drill bit and drill straight through the middle of the lexan and two pieces of wood (just a small hole) so you'd know where the center of each button was. That way aligning your hole saw bit would be easier on the last board.