It depends where you want the plexi to end up.
The mounting plates hole, fits around the lib of the trackball. so if you did not purchase the high lip trackball, you could cut the plexi smaller than the mounting plates hole.
I would recommend beveling the plexi to prevent your skin from pinching, Mountain (I beleive) has some real nice photos and descriptions of his trackball where he beveled it. he used the mounting plate as a guide for his router and it fits perfectly around the lip of the trackball. very nice job.