[davepl]

It varies by transmission and it does matter, I'm told. TH400 is backwards from 200-4R, for example. 4L60E return is on the top. 4L80E is on the lower. And so on...

Any blanket statements about which way it goes without being specific to your model of transmission has about a 50/50 shot of being right.

USUALLY though, and this is a gross generalization, I've noticed that they're typically laid out so that the lower port goes to the lower port on the radiator. That might not be 100% though!