When I routed the holes using the NFM template I made sure it was level with the cabin top. Some boats have a large smooth radius cabin top so you'd need to find a way to measure for level but my boat has a nice square, clean edge to work off of.
Before applying the butyl tape I made sure to line up the ports and make sure they were level by using my combination square. Once they were level I tightened down hard on the clamps making sure to use a block of wood on the inside to prevent scratching the port.
This photo shows me checking the right side of the port with the combination square.