In my opinion they are a real pain in the butt. First make sure you have the original LN-Builder database. Assuming JCI installed the first set. If you don't you will need to build one with all the new units, the old units and the NAE. Once they are commissioned in LN-Builder I'm not sure if you can auto discover the devices I'm pretty sure you can, but you can definitely auto discover the points.
That is the beginning of the problem. Unless Trane has changed their system when you auto discover the points you will have duplicates of most of the points and you will have some points that don't work at all. This is due to the way Trane does their LON systems. The problem with the NAE is that you cannot have 2 duplicate identifiers. So when you do the auto discover you will have to go through and change the identifiers of the duplicates. I usually just add a 1 to the end of the point. Then just go through and delete what isn't working.