So originally I had planned to do it this way. I am not a roofer either, but I have seen most done the way you show. The guy who I had that day did the first one by the method that we ended up going with. I thought it looked ok so we did them that way. I laid the pipe jacks so that if the shingles were cut away it would look like your picture. If I have a leak I will go straight to that...We got 2 inches on Friday and I did not have any problems....and that was with half the roof in tar paper.