I'm guessing that by bulkheads you mean the forms that you are going to build the boat around. It sounds like you're on the right track. The forms should all be square to the strongback, both vertically and horizontally. If you draw the waterlines on the forms, the waterlines should define a plane parallel to the strongback. Often it is convenient to make the bottom of an internal strongback (Guillemot-type) correspond to a waterline, which does not have to be the actual waterline of the finished boat, it just represents a plane parallel the actual waterline and a given distance, maybe 2 or 4 inches, away from it.