[87Skier]

It doesn't matter, but I put the hot side (being pumped out of transmission to cooler) on the higher port of the cooler, and the return side on the low side. The thinking here is that it doesn't need to be completely full for fluid to get back to the transmission if the cooler isn't completely full.

Really it shouldn't matter though, since having a empty cooler would mean that the ATF isn't being cooled, but I would rather the transmission has enough fluid to operate than to worry about it being low on fluid and the fluid being too hot.