This is a good project to try some new things. I'll give you a couple of tips that you might consider.
First, as was said above, balsa is not your best choice for modeling wood. It's way too fuzzy and if you stain it it will really lift the grain. The better choice is bass wood. Or another hardwood veneer, if you have a little table saw. I would also say that it's only worth planking the gun deck under the open boat beams, and enough fore and aft to give the effect. The center plank is wider than the others, and there's a pattern to the placement. I'm not familiar with the Constitution, but the info should be easy to find. There's a tip I haven't tried, to rub all the edges of your planks with a pencil to simulate the caulking.
You will need to cut off the bottoms of the gun carriage trucks, or better yet not plank where the guns go, in order to get them level all the way fore and aft.
One other thing well worth doing is to build up the thickness of the hull at the gun ports. The top of the opening isn't important, but the sides and bottom should have a square piece of styrene or wood, say 1/16" thick, glued flush around the inside edge. If it's even visible down through the boat beams as an add on, it'll be dark in there, and everywhere else it will add a great deal to the look of the boat.