Jay since you are using a non-adhesive overlay and covering it with plexi you should have no problems with the joy plates/trackball affecting the artwork.
When I use an adhesive overlay I do like to put cardboard spacers in the recesses on top of the joy bases, so the overlay doesn't sink into there and get stuck. I never had this happen with any of the earlier CP's I did using paper overlays though.
As for securing them I use #8 32x1 1/4 tapered head--> \ / machine screws with suitable lock-nuts and washers. These screws will sink into the plastic joy plate as you tighten them.
Insert a screw into each of the 4 corners of the plate. Then from the underside of the CP attach a washer and lock-nut onto each screw. Tighten them with a screwdriver and pliers/nutdriver until the screw head is sunk just below the top of the mounting flange.
BTW Tim has a good guide for making router templates, it's stickied over in the Woodworking forum.
