The first time I took it to the dealer and they exchanged the fluid with the TransFlow machine. The machine does a flow test on the transmission cooler and lines and then lets the transmission's pump do the work of removing the old fluid and introducing the new fluid into the system. The second time I did it at home, took off the top line from the transmission and let it flow into a bucket, then added fluid through the dipstick tube. Again, the transmission's pump did the work.
Decide whether or not you want to turn off AFM and either way, I recommend that you get the truck tuned by BlackBear Performance. Not to go faster but for improved transmission performance. Get yourself a Tech-2 so you can properly diagnose and work on your truck too. After the fluid is changed, you can reset the internal transmission oil life meter with it.
If this is a 4x4, do you have a single speed transfer case or a 2-speed TC? Does it have RPOs K5L, KNP and KC4?