With any genre of modeling the instructions are only a guide and you must read the instruction sheet(s) thoroughly with the thought in mind of when to paint and when to wait. I firmly believe most kit mfgs believe most buyers never paint their models.
I am in the early stages of a WW2 cruiser build. The instructions show adding small parts immediately as one builds an area. I prefer to leave most small individual pieces off if they can be glued on later, especially if they are not the same color as the pieces they are mounted to.
I generally paint the hull and deck seperately and then glue them together. The trick here is to check fit of deck to hull carefully so the resulting seam has no gaps after gluing. Correct any gap areas to try to avoid needing putty.
I generally paint major superstructure assemblies as I complete them, before gluing to hull/deck assembly. If I am using PE, I try to paint as much of the PE as possible while it is still on the fret, and glue it on already painted. While I paint major pieces with an airbrush, I find it easy to paint very small pieces by brush. It is a pain to have to mask off small pieces, or the area around small pieces. So if there are small fittings on, say, the deck that are different color than deck, I paint these by small brush after airbrushing deck.
These are only general guidelines. Painting a ship model may be the hardest genre to paint, and you need to do a lot of thinking ahead and planning and visualizing.