Operating question

[nachoman]

I'm with David here. I'd start with the tracks empty, and then let your operating scheme evolve into what feels right for you and for your layout.

Remember, it is impossible to operate a model railroad exactly like the prototype because of compromises we make:
1) We have no real connection to the outside world.
2) Our model freight cars don't really carry anything
3) Spatial compression.

In the real world, different railroads may have had different procedures and different crews may have had different preferences as to how to switch cars. Many of the things we do to operate our layouts are to simulate real world scenarios. In your case, yard tracks are probably sometimes empty, and sometimes full. The railroad may be storing extra empties sometimes, may have MOW cars parked there sometimes, or there may be a delay on the main line connection that requires the cars remain parked for an extra day. If you are using a card system, perhaps you could design scenario cards that tell you what is on each yard track on a given day.

When I eventually design an operating scheme for my layout, it will be a mix of what I think is logical, what the real railroad did, and what is necessary for my layout design (lack of a staging area, etc). I don't expect my scheme to be perfect from the start, and expect that I will have to let things evolve as I operate it a few times.