Get one of those cheap hobby knifes with the snap-off blade sections (hopefully that makes sense). Use a template like btp2k2's, and use a whiteboard marker to mark dots onto the styrene. Then get a candle. Drag the knife edge across the candle - this makes the blade slick and less likely to hang up in the styrene.
Plunge the blade down about halfway through an edge where you want to cut, then cut both ways to complete the side. Re-wax the blade frequently. Repeat for the other 5 edges, and with a little care, voila! You've cut your hole. I used this technique to make these.
Did the waterholes that way - then sliced the top 1/4 off the plug, and glued them back in place. Which reminds me, I need to run a Quick-Strike game sometime ;)
W.