I haven't had the privilege of using one of these yet either, but the idea behind the clear ones is that you don't have to make cardboard templates and "guesstimates" about where a hole should be cut.

You need to remove the muffler and the needle valve, and other parts that impede with installing the clear plastic cowl. (Not sure what you'd do if the head prevents installation. )

With the clear cowl mounted, you simply draw where you need to make cutouts on the surface.

Form here on I'm guessing. You remove the clear template cowl, cut out the areas you marked, place it back on to make sure of the fits, then place it over your painted cowl and trace the cutouts onto it. (It's kind of like 3 dimensional cardboards templates.)
Dennis-