Cut out metal only after you have your patch panel in hand. Place it in the trunk and mark where the seam is all around it. Your measurement here is critical. Use your flange tool to decide how far below your marked line you should cut the metal: if the flange is 3/4" then cut 3/4" below the line.
To cut the panel out you can use an angle grinder with cutting wheel. My favorite is the Makita pictured here. I like the smaller 4" model best; I also use this to do any grinding later. I also make use of an air hammer but you don't necessarily have to use one.
