It's just a small cooler inside the radiator. It will perform the same operation either way you hook it.
It is my opinion tho that IF you should want to use a external cooler and tha radiator, you need to know which way it flows. I like to run the fluid thru the external first then thru the radiator then back to the trans...again, my opinion.
When using an external cooler you should always run the front line from the transmission to the radiator and then from the radiator through the external cooler and back to the rear transmission fitting.
Blugene, The transmission should be running cooler than the engine. The optimum temp for a transmission is 170 and your engine runs at nearly 200. You are using the transmission to cool your engine first while the temp differential is low and then cooling the fluid going back to the transmission. If you put it through the radiator after the cooler you will be heating the transmission oil just before it goes back to the tranny. It is better to cool it just before going back to the transmission.