You should want your fan pointed to the greater air source which would down towards the ground. No prob installing inline, just do a flow test when your done, you should see 1 quart every 15 sec at the return line to the trans.
Can I ask you a question? Why are you bothering installing this fan powered unit and not just install the cooler out of a 6.0? My temps dropped 40 degrees and it bolted right in the same place as the stock cooler. Took less than a hour to do. You can also use the one out of the V10, it isn't as big as the 6.0 but larger than stock. I don't have the cooler in the rad and the warmest I have seen is 170 in 95 degree ambient and towing heavy up some slow steep switch backs.