I've done muffler cutouts a couple different ways. If it's for a 2 stroke and the muffler cutout is fairly close to the back of the cowl, I cut a slot to allow me to slip the cowl around the muffler. On a 4 stroke I've made the hole large enough to let the muffler exit the cowl and removed the muffler before attaching or removing the cowl. Note that there are also flexible muffler extensions for 4 strokes that would allow you to route it to a more convenient, less obvious, place.