For some reason this particular kit seems to be popular among Forum participants at the moment. We've been discussing it in several threads lately.
For the benefit of anybody who hasn't been keeping a score card - the identity "Jolly Roger Pirate Ship" is a marketing ploy on Lindberg's part that has nothing whatever to do with historical reality. The kit is a reissue of a 1960s kit that represented - reasonably well - the 18th-century French frigate La Flore.
I guess the "proper" color scheme depends on what one is trying to do with the model. If you want it to represent a "pirate ship," you have unlimited artistic license. It's highly unlikely that any actual pirate ship ever looked remotely like an 18th-century French frigate; since this is a work of fiction, the modeler may as well paint it however he likes.
If you want to build a model of La Flore, your best approach is to paint the "bare wood" portions of the hull above the waterline to represent bare wood. A medium to dark brown, with a yellowish or orangish cast, probably would be appropriate. (One school of thought says that the oil used to treat hull planking turned black over time, resulting in hulls that looked like they were painted black. I have my doubts about that one, but I guess it's possible.) I'm not really familiary with French painting practices of the time, but I suspect the wales (the wide belts of thick planking just above the waterline on each side) were black. The decorative moldings might have been yellow ochre or black, I imagine. The exterior planking of the bulwarks might have been black or blue (maybe somebody who's studied French paintings and drawings more than I have can help us out here), and the carvings at the bow and stern might well be gold.
Several treatments for ships' bottoms were in use in the late 18th century. "Dark stuff" was a chemical composition designed to ward off marine growth; it apparently was a remarkably ugly brownish, slightly greenish black. "White stuff" was white lead paint with various other substances mixed in with it; it probably would be a brownish, yellowish off-white. (We've discussed this subject fairly recently in the Forum; at the moment my halfzeimer's-afflicted brain is having trouble remembering the title of the thread. If I remember I'll edit this post.)
That's about the best I can offer. Good luck.
Hope that helps a little. Good luck.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.