Trebor, there will be several answers so brace yourself. Most will say to paint subassemblies, the hull and deck seperatly prior to assembling. I do this and have been since I started building ships. I've lately discoverd black basing and use that method as a primer, and can an usually will, apply the black primer on the sprues. This insures that the crevases of the superstructure ETC. are painted. I will then go over the subassemblies with the base paint, and/or camo, depending on the ship, and hand brush the small fitting and such located on the deck, bulkheads prior to final assembly, rigging as I go.
On modern ships I have taken a diffrent tack lately. I assemble the entire thing, all but rigging. and spray the whole thing black (I have already sprayed most of the parts on the tree) and then go over with the base paint. Since modern ships are the same color, except for the deck, I'm finding it a little more realistic. I do have two air brushes, one with a .3mm tip, and the other with a .15mm tip. These allow me to do this around the deck and such. The result is a uniform color, very little seams and some wear showng allowing the dark shadow areas to remain that way.
Here is a pic of my last years build of the very OHP you have unsing the method I spoke of.
