Two things you can do:
BYPASS: You completely bypass the factory cooler. You hook the lines coming from the tranny directly to the aftermarket cooler, the fluid is cooled, and returns to the tranny.
Benefits: Cooler transmission fluid (always a bonus), reduced radiator load.
Cons: You'll have to install a temp guage. The factory cooler has a built-in thermostat bypass that keeps fluid between a certain temp. If your cooler were to fail, you wouldn't know until it's too late, so a temp guage is recommended. You also run the risk of "overcooling" your tranny in the winter if you get cold winters in your region.
SERIES: You run the fluid from the tranny to the stock cooler, then to the aftermarket cooler, then back to the tranny.
Benefits: Keeps the tranny cooler by an extra 5%, recommended by engineers, maintain a cooler tranmission within recommended levels.
Cons: You may have to buy additional fittings if your cooler didn't come with them. Extra load on the radiator because you keep the stock cooler...