Here's my order of battle for a typical ship kit...
Paint the deck.
Paint the hull.
Attach deck to hull, do required touchups.
Assemble bridge, funnels, etc...in subassemblies, paint accordingly.
Build and paint PE assemblies, attach to any parts that are not already attached to model, like railings on the bridge, etc...
Attach subassemblies, then photoetch, making sure you work from the centerline of the ship outwards. The rigging comes next, followed lastly by the rails, then some weathering, drybrushing, etc. If you want heavy weathering, consider doing it while the model is still in subassemblies.
Jeff