You didn't exactly mention what ATS configuration you were purchasing but make sure you get the torque converter and the commander module if you buy the ATS transmission. The commander module allows the transmission to look up in at least third and provides some engine braking capability.
For what its worth, my daughter recently went through this same delelma. Problem is that if your original transmission is trashed, it cost almost as much for a Dodge replacement as the ATS and ATS has a much better warrenty. On top of that, we had ATS do some other work on the truck and they have been extremely good to work with and totally stand behind their products/work.
Just a thought, if your transmission isn't totaled and you know a transmission shop you trust, you might want to go with just a ATS torque converter and a valve body during a rebuild. From what I understand that may be enough to address the majority of the transmission problems if done in conjunction with a transmission temp guage.