When using a transmission cooler on a high performance motor do you run the trans lines to the cooler and back to the trans or do you run the line to the cooler then into your radiator and back to the trans? Which set up is best?

 

run the cooler only. keep it away from the hot coolant. plus if your radiator ***** it wont mix coolant into your tranny and vice versa

 

Kind of like the paper or plastic question, ..., or the Auto versus Manual question, ...
I'd have to say that one option would be from transmission, to radiator, to cooler, back to transmission.

 

I ran mine in series like pontiacfan described...it also kind of depends on what weather your car will see and what type of cooler you get. My cooler does not have the the low temp bypass feature, so I kept the stock cooler to help heat up the oil on colder days to make it easier on the trans. If you run it in series, stock one first followed by the external cooler.
I posted pics of my set-up in a different thread in this section awhile back.