Kalmbach has a book written by Mike Ashey that's a must have. Most of your better hobby shops will carry it.
Building a ship model is only slightly different than doing armor...build your superstructure in subassemblies, and don't attach it to the deck until you're ready. Paint your hull first, in the case of Indy, she wore Measure 22 at the time of her loss. What this means...is stretch a line from the deck edge at the stern, and run it parallel with the waterline.everything below that line is 5-N Navy blue, everything above it is 5-H Haze Gray. Paint your superstructure, turret sides, etc., 5-H Haze Gray, and paint all horizontal surfaces, turret tops, decks, catwalks, etc., 20-B Deck Blue.
Best advice is to work from the centerline of the model outwards towards the edges. This prevents you from knocking details off reaching over or in towards the center of the model.
Since Indy hadn't wore her Ms22 for very long, she won't be as weather-beaten as you might think, so keep your weathering, rust, etc., to a minimum.
Let me know if you need any photos, etc.
I would also recommend the Classic Warships book on the Indy...
Best,
Jeff