You want "push button" convenience? As long as money is no object, then I suggest an electric filing system adapted for railroad purposes in which you could store entire consists and retrieve them with the touch of a button:
However, if such is out of your price range, then I concur with the storage drawer concept with tracks aligned perpendicular to the direction of drawer travel in opening and closing - you don't want to be charged extra mileage on those privately owned freight cars every time you open or close a drawer. Shelving is always precarious and a derailment could ruin your day.
As far as a staging yard, I'd suggest a double ended facility so that you can enjoy the convenience of not have to make extra moves to yard your trains. You'll want to not only stage and run your trains, you'll also want to re-stage them without fuss or distraction.
However, let me suggest something to increase interest in addition to running more equipment: way freights. If you can program your "through trains" to operate independently, which it sounds as though you can, you put the through trains on a timetable and then operate way freights, ducking in and out of sidings to serve customers and clear superior trains - just like the real thing.