It was the final drawing right-side up. He had the prop department knock up a smallish model of it to push the design he favored (which is what we finally got) but the saucer and engineering hull were made of balsa and the engines were birch dowels (they had a pretty short time frame to finished model). Since the dowels were heavier, the model flipped over on it's string and Roddenberry really liked it that way and MJ had another fight on his hands to get it turned back right-side-up.
True story!
--Alex