Hi Chris,
If you are using round aluminum panels, simply measure and go for it. If you have decided to go with the square ones (which I did - 16" square actually) you can use a 'follow' router bit. I simply use a 1" chipper bit and drill a hole 'inside' the module. The 'follow' bit has a wheel on the bottom that follows the inside walls of the module and routes the appropriate hole in the 45x45 panel. Now hopefully its obvious that only 3 sides will be able to follow the module sides. I make the router cut along the back side of the module first, and then run the router about 6" up each side of the module. then I stop and, using a square placed along the back 'rout', measure out 11" from each end and connect those two points with a line. I then run the router along the sides out to that line, finishing those cuts. Now its just a matter of tacking a straight piece of wood the proper distance out from the line to use as an edge to run the router against to make the front cut that isn't against a module sidewall.
If you've followed this so far, let me make another suggestion. Again I am making the assumption that you are using over-sized square aluminum panels. I made a square template 22 1/2 x 22 1/2 which is the 16" of the panel plus 2x the offset of my router (you may need different measurements) and the bit I use to countersink the aluminum panel. I carefully temporarily tack the template in the proper location and do the countersink BEFORE I do the last cut to open the access hole. This leaves me a bigger surface to support the weight of the router as I do the countersink and makes it a bunch easier to control.
Hope this helps = of course if you're doing them round, well, nevermind! lol
Al