Bish,
Actually, I think every ship builder paints and builds a bit differently. In this case, I am going to paint the decks first and then paint the structures on the deck next since it is easier to mask a horizontal surface than a vertical.
Once those are painted then the hull colors will be painted on the lower hull and the flying deck. After those dry then I'll add weathering to everything. After this I'll go ahead and glue the flying deck to the main deck. At this point, all the superstructure and turrets will be built and glued on. I plan on replacing the masts with brass rod since the plastic masts won't take a strain, even with EZ line.
Since I normally rig sailing ships, this will be rather mundane except that I have never used EZ line before.
Steve