I'll give you several options for painting the decks
1) Mike Ashey in his book Basics of Ship Modeling by Kalmbach, assembles the kit to the deck stage and paints the deck. He then masks the deck leaving the bulkheads and all the deck fittings exposed and sprays them. It is labor intensive, cutting and placing hundreds of little snips of masking tape, but it looks very nice when complete.
2) Another method is to paint the deck by spraying vettically down on the deck so as to minimize any overspray on the bulkheads. Spray the hull and bulkheads by tipping and holding the hull so that the airbrush is below the level of the deck. The deck edge masks the deck and allows you to paint all bu the bottom quarter of the bulkhead. Hand paint the bottom of the bulkhead and the deck fittings.
3) See the article on SteelNavy on masking and painting decks to acheive a random planked pattern.
http://www.steelnavy.com/wood%20deck.htm