I just did a bunch of research on this before I mounted all my coolers...My understanding is if its a BIG tranny cooler and its mounted high up in the vehicle.. I.E. hammers buggy with giant duel coolers mounted where the back window would be..then you should mount the cooler with the ports up to avoid any drain down and overflowing of the transmission which could cause a leak. If its the relative size of the factory cooler and the same relative height as the factory location, then it doesn't matter which way the ports are. Transmissions are good at moving fluid in both directions. Power steering pumps are good at pushing, but the suck at sucking..thats why the cooler/ return line for power steering needs to be short, straight and as close to the pump as you can get it.