Since I am about to attempt this in the coming weeks, I thought I would post the steps to take based on the comments by Markrvp to make sure I have the process down right:
1) Cut the diagonal diamond shaped hole out of the CP required to house the trackball (Jigsaw).
2) Drill 4 holes for the mounting plate
3) Place the plate in the 4 holes and trace around the mounting plate
4) Remove plate and freehand router out the shape you just traced to the depth of the plate (roughly 1/16) by either setting the plunge depth to that depth(if you have a plunge router) or setting the bit to that depth.
5) Flip the plate back over and let it rest in the space you just routed with plate posts in the holes your drilled earlier.
6) Lay your Lexan over the CP and clamp it down tight.
7) Drill a hole in the lexan

With a finish bit, use the trackball hole as a guide and route out the lexan flush with the shape of the circle in the plate
9) Unclamp and attach trackball to mounting plate
10) Lay CP overlay using spray adhesive
11) Attach Lexan on CP
By this logic, it should appear exactly like Markrvp stated. The lip of the track ball should be exactly flush with the Lexan.
Sheesh this board is invaluable. You must always say to yourself "Someone must have already done this before me"
Thanks guys!