Andrew,

First install the engine on the motor mount in the plane. Then, take a piece of craft paper, index card or other heavy paper and tape it to the fuselage on the side where the engine will be to make a template. Make sure you tape the paper behind where the cowl will mount. Carefully cut the paper around the engine and everything else that will stick out beyond the side of the fuse. When you are satisfied with what you've done, then simply lift the paper and fold it back. Then install the cowl, lay the paper template over the cowl and mark it. Finally remove the cowl and cut the hole for the engine.

David