I ended up having to do plexi since there was a mistake in putting on my overlay that left a little bit sticking up. I'm going to redo it but in the meantime, I put plexi down so it annoyed me less.
I don't think I did anything terribly fancy or complicated (then again, my panel is a simple rectangle) - mostly what unclet said. The same drill bits that cut my panel's holes cut the plexi fine. I just clamped it down to the CP, reverse drilled some pilot holes, clamped it down to scrap and alternated between reverse drilling and slower forward drilling. And to cut the plexi to size, I used a plexi-cutting blade and a straight-edge.