^ The first scenario (i.e. I clamp down the plexi and then clamp the CP on top of it). That way, it ensures that the holes in the plexi perfectly line up with the holes in the CP.
Also, here's a sample template and how I use it:

I top-mount my joysticks, so the template has two parts. The top is the cut out for the main joystick body; the bottom part is for the mounting plate. To route out the joystick, I do the following:
1) Mark the center of the joystick on the CP piece, and then draw horizontal and vertical lines in a crosshair style so the center of the crosshair is the center of the joystick.
2) Line up the crosshairs with the pencil lines on the template, and clamp down the template to the CP piece (template on top). I start with the top part of the template (the main joystick cutout).
3) Trace the outline of the joystick with a pen onto the CP piece.
4) Remove the template, and then using a combo of a jigsaw and drill, cut a rough size of the joystick cutout, making sure to keep
within the lines.
5) Reclamp the template on top of the CP piece and using a top-bearing flush trim bit, route out the hole to the exact size of the template cutout.
6) Reclamp the template to the CP piece so that the mounting plate part is lined up.
7) Again using a top-bearing flush trim bit, route out the area for the mounting plate. Note that I only need to go down about 1/8 of an inch or so.
The end result is a joystick cutout that looks like this:

This is specifically for a top-mounted joystick. If you are bottom mounting, you can either just recess an area for the top mounting plate (if that is all you are mounting), or possibly both the top mounting plate AND the main body of the joystick. It depends on how deeply you want the joystick recessed. Also note that you'll have to do things in the opposite order listed for top mounting. IOW, you'll need to route out the mounting plate area first, then possibly route out additional space for the main body of the joystick.
Also, note that this is entirely dependent on the physical characteristics of the joystick.