It doesn't make any difference, but on the car the rear pipe on the box is the return, which runs above the front one which is the supply to the cooler, and so if they stay the same way up to the rad then it goes in the bottom fitting, and out of the top, but as I said it actually make no difference. That's the orientation of the pipes on a 35 box, 65 may run differently as the cooler fittings are on the other side of the box, (rear is still the return though) but the same applies. Both the feed and the return are running at the same pressure, it can't lose pressure just running through the cooler.