I've always plumbed an input into a lower port if it was available. That way it seems that any air would be forced out the top and not create a pocket.
Probably not an issue with a trans, but that's how I think of any type of fluid line.
And there is a school of thought too, that says to run it through the auxiliary first, to give it an initial cooling, then on into the radiator. That way, if it's hot, you're not putting any more heat into the radiator than you have to (although the heated air from the aux cooler is still going through the rad), and if it's cool out, the engine heat will normalize the heat in the trans.
Nothing scientific in what I said, but we've had discussions here and on the full-size boards over the years about the "which one first" debate.
Paul