James, the rough game plan is to mark the mortises with a gauge and then chop them. Next, you use a gauge to mark the tenons and saw, split, or gnaw them, but stay a bit fat. The final step is to use the router plane to fit the tenon to the reality of whatever each mortise turned out to be.
Paul recently has been using a method that makes the mortising jig from the frame stock. This may be a good method for doors, which need to be true and flat, which is helped by having a hand-in-glove fit. I’ve not tried this new method and still use his older technique, although I’m about to make a pair of doors, so maybe I’ll give it a try.
Hope this helps. If it wasn’t clear, you never set the router like you would set a rabbet fence or gauge fence. When you first bring the router to the work when the tenon is fat, you’ll lower the blade until it just kisses the tenon. From there, you’ll drop maybe 1/4 to 1/2 turn of the depth screw on each pass until you get to a good fit.