Can I just say, to begin, that I cannot BELIEVE that this $100 Arf came with a plastic cowl template to use? I could not belive this morning when I picked up the cowl from my World Models Super Sports 40S box, and said "HOLY CRAP!!, They Included a overlay!!". My $200 Sig Kadet Senior that fell apart mid air didn't even come with one of these!! And, the cowl is painted NICE!!. I'll tell ya you cannot beat these world models for the price..

Anyway, I have never used one of these overlays to do a cowl cut, can someone explain the best way to go about it?

put it on and mark it , tranfer to painted cowl. bingo.

To be more precise, mount the transparent cowl just like you would any cowl but without the needle and muffler.
Use a marker and mark the holes you need to cut and cut them out with a Dremel. Slide the 3D cowl over the glass cowl and outline all the holes with your marker and grind them out, again with a Dremel. Your done.