There will come a time when you want to override what the program assigns as shipments to cars. In fact, the first time you actively run the program with your layout, you may want to seed some or all the cars where they sit, as opposed to moving all the cars to where the program thinks they are.
In the Administration form, selecting any empty car, you will see a button far right "Assign Shipments". Pressing this button will display a list of possible shipments that car can do from the total list of shipments in the database.
The list displays two sections, primary commodity list of shipments, then secondary commodity list of shipments. Any shipments it finds that are from where the car is physically located will be bolded, but you can assign any of these shipments to that car. The Heading To is where you want the car to go to to fulfill the shipment, Came From, if bolded, is where the car is now, otherwise it can be any of the locations indicated. Frequency is irrelevant for this assignment as it will be assumed to be ready for movement immediately (unless you change the pickup date).
If you change the location of a car first, say from a yard to an industry, make sure you update the car first before assigning a shipment to the car.
In other parts of the documentation, you will have noticed that if a shipment is required a car can get seconded to facilitate that shipment. You can simulate that here too. For example, an empty boxcar in a yard you want to send to an industry so it can be filled and sent elsewhere. If you select the shipment the program will assume the car is full and ready to go to the destination, but that is not what you may want. What you want is to start an empty transfer.
To do this select the shipment for the car, return to the main form for rolling stock. Top right is a button marked "Make Empty Transfer". Hitting this will change the car to empty and you will see the destination is no longer the loaded car's, but the place where the car is to be loaded.
Thus you have free reign in presetting your layout anyway you want. This will be most helpful in initializing the program. You can set up the system without moving all your cars on the layout to the default yard.
Keep in mind, this not a replacement for the program automatically moving cars, but a tool to manage or manipulate car movements.