the best method i have used is to take a pencil and chop the last inch of it off.
sharpen the pencil and then rub the pencil on a piece of sand paper so that the long edge is flat.
once you have a flat run, glue the pencil to a small piece of scrap ply wood [1/16 or 1/8th thick so that the lead point protrudes over the end of the little piece of ply wood.
. then you can run the pencil around the deck with the superstructure taped in place to stop movement.
you get a perfect parallel line of the deck marked on the superstructure, which you can then file down to….giving a perfect fit between deck and superstructure.
voi’la
neil