Zcruiser: this thread has the lines labeled, just follow the hard lines from the trans to see which is which... TRD Transmission Cooler - 3rd Gen 4Runner - YotaTech Forums
That's up to you and people will argue till they're blue in the face for both ways so good luck...
I put my line from the trans into the top of the cooler. If anyone thinks the bottom would be better, do it that way. This isn't even considering all the people who would say the cooler should be positioned with the inlet and outlet pointed up or down.
Edit: However, the fact that you use Guinness as your avatar makes me think you are right about pretty much anything.