See how i have mine setup. It may help you:
I have one location called "Northeastern yard"
In that location?I have tracks designated as below:
6 classification tracks designated "Classification/Interchange" in the program that allow everything but engines, cabooses, and passenger cars
1 RIP track designated as a "Spur" with a schedule to randomly pull a car that allows everything but engines and passenger cars
1 Caboose track designated as a "Yard" that only allows cabooses
1 Supply track designated "Spur" that only allows Sand and Fuel cars
6 Tracks for the engine terminal designated as "Yard" that only allow engines.
1 Track that is the yard switcher pocket designated "Yard" that only allows engines that are switchers
As this is all one "location" it has never had a problem with assigning engines and cabooses or getting them all in the right place at the end of a run. I also do not designate arrival departure tracks as they vary as needed. I do however have the classification tracks limited to certain trains/routes/locations so when the train comes in at the end of the day the program tells where to put them to be in the right place for the next trains out.?
When my trains come in I pull them into the "arrival/departure" track(s) (which vary as I need them) and I cut the road engine loose and bring it into the terminal. The yard switcher takes over and puts everything else away, but it not mentioned at all in the program. The system still needs some human intervention to sort out the best way to do the actual work. It just tells you what has to end up where, not how to actually accomplish that.
I think you may be overly complicating things on your setup. Try simplifying first and then add more restrictions as you get used to it.
