This question of how to position a board on the car roof rack crossed my mind too. I have seen many people putting boards upside down with the front of the board pointing to the front of the car. It may look good as the board's shape follows the curve of a car's roof. But I think this will actually cause more drag hence you will get less milage per litre of gas. If we were to think of the aerodynamics of a board, then a board on the car roof would behave more like a spoiler if the board is placed with the tail of the board pointing to the front of the car and with the deck of the board facing up. Another reason why I place my board in this manner is to prevent possible damage to the bottom of the board.
One thing I don't do is to leave the fin still fixed on the board when I transport my board on a car roof rack.
Any one with a good understanding of aerodynamics care to share your thoughts on this?