Dan, the top line on the transmission is the pressure line (to cooler) , the bottom is the return (from cooler). You'll have to go under the jeep and see which side of the cooler the pressure line gets into, I don't remember on the top of my head. There were some members that cut the integrated cooler out from the condenser, I personally think it's overkill. If you do decide to go that way, there are some coolers that you could fit in that space (
http://derale.com/products/coolers/tran ... /heat-sink) but you should also consider adding an extra one as papaindigo linked. Btw, it doesn't matter which line is the pressure and which is return if you're not thinking to add any temperature gauge on one specific line. I'd advise to use a cooler that is not serpentine since is more efficient. Also, a bigger cooler is better, the transmission has a thermostat inside, so you won't over cool it even if you want to.
My approach was to remove the electric pusher fan and add the biggest transmission cooler I could fit (TRU COOL 47391), you can buy it from eBay cheaper (
http://www.ebay.com/itm/like/261236299635?lpid=82). It is a lot of work though, you also need to add 2 fans, the only ones that fit are 7 inch wide, in the pic below you can see an installation pic with one fan.
I decided to totally bypass the factory cooler as a preventive maintenance, since I can see those fittings being prone to leaks.
I'd say this is overkill if you don't tow regularly, but my temps rarely go over 150 degrees in the summer under heavy city drive. In fact I only saw it getting to 150 in new York City while driving very aggressive for about 2 Hours going from Jersey to Manhattan in traffic. Here in Cleveland, it gets to about 120 tops.