Is the superstructure separate or part of the deck part?
Check how the deck attaches to the hull. If it sits down inside it, paint the hull and the inside of the bulwarks gray before attaching the deck.
Paint the deck blue. Mask around the base of anything thats molded on the deck, and either handpaint those gray or mask the entire deck and spray them. Masking decks sounds tedious but its not hard as it's just a big flat surface.
If the deck somehow includes part of the bulwarks, or the edge of it is exposed, you'll have to put them together and figure out a little more complicated plan for masking.
Paint as much as you can in assemblies separated by colors.
I usually make a photo copy of the part tree illustrations and mark which parts are which colors. For a trumpie model that has about a squillion parts, it really helps.
My Midway on the other hand- old school. The plan is one sheet of paper, model instructions on one side and ads for other Revell kits on the other. Single exploded view and a couple of notes.
Thank you for the kind words about her.