So let me get this straight. You have a dealer, so are you going with one of their homes? If so, you should be able to do anything you want. If you don't want the upstairs finished, but want the plumbing roughed in, get it done when the house is ordered. If your particular manufacturer sets only two boxes instead of three, so be it, and the finish carpenters will do the roof and rough in the knee walls if you wish. Just have them put down a subfloor over the insulation so you can finish the rooms later.

If the dealer is the builder he should be the general contractor for all the things I mentioned above and you should get a finalized set price before signing anything.

As far as drawings, you should get a complete set from the manufacturer when the boxes arrive if not before.