Because of the complexity of staging yards, as discussed in Staging Yards, shipments to and from such yards needs to be discussed separately. In the Shipments menu, Staging Yards tab, you will see two grids and a list. The top left most list shows for each staging yard and car type how many shipments there are going into the staging yards. The bottom left list is the same information but for shipments going out. The right list notes any problems, as per discussed in the Staging Yard page.
Two possible problems can exist, depicted in the display above.
First let's look at the problem. You will note that Lambton Staging, a staging yard, has 1 boxcar shipment outbound and one gondola shipment inbound. Notice that at this point there are no box cars that enter the staging yard. That is, no shipments into the staging yard of boxcars. This is a serious problem as if no such cars enter a staging yard how can the staging yard send the boxcar shipment back out? Notice also that the gondola car does not have outbound shipments of gondolas. The situation between tank cars is balanced. One tank car in, one tank car out (both of the same commodity, liquid chemicals).
Notice the right list contains the specific problem so you do not have to search between the two left lists for discrepancies. The critical one problems, like the boxcars, is in red to draw your attention to it. Clicking on each one of the problems will allow you to fix these problems.
The top problem that is not critical. You can make a bridge shipment for these outbound cars instead of trying to make specific shipments. The program will make this bridge shipments for you. You can make a bridge shipment from any staging yard to any other yard that accepts shipments, including other staging yards. If you choose to do nothing with this, these hoppers will emerge from the staging yard as empties.
The critical problem requires intervention or the shipment will just not happen at all.
In this case, of the box cars leaving a staging yard, the only solution is to send empties on the train that goes into the staging yard, should one exist. You are actually creating an empty transfer to a staging yard so the inbound shipment, in this case the boxcars, can emerge as an outbound shipment. Thus the only yards in the right list are yards that store empties.
With all this said, you can still manipulate cars in a staging yard. You can remove cars, add cars, even create a whole staged train. In the Administration form there is a button top right for managing staged trains (You can also access this button on the Run Scheduled Trains page.)
This form contains two tabs. One for current trains in staging, and one for making a staged train or adding cars to an existing staged train. The top list of trains will display trains currently in staging with cars and virtual trains that have yet to have cars assigned. Virtual trains are any trains that start at a staging yard. The problem with any train that starts at a staging yard is getting cars onto the train. There are two options. Either manually assign cars as per below, or you can transfer cars from one train to another. For example Train 1In comes into staging with 10 cars. You have defined Train 2Out and Train 3Out as trains that start from staging. You can transfer Train 1In to either of these two out of staging trains, where upon Train 1In no longer exists at that yard. You will be able to transfer any in to staging train to any other out of staging train on the layout, including different yards.
You can also remove any number of cars from a staged train, as well as reassign locomotives. In the bottom portion of the Staged Trains Out tab, there are two sub-tabs, Cars on Train and Locomotives on Train. Selecting a train from the list of staged trains at the top will display either the cars or the locomotives on the train depending upon which sub-tab is selected. To remove a car, select the car and then select the Remove Checked Cars From Train button. The proceed is the same for locomotives on the locomotive sub-tab. You can also add locomotives by selecting a locomotive and then selecting the Add Locomotive to Train button.
To create a staged train manually, select the staging yard. You'll then see a list of cars and the yards they are at (thus you can manually place any car in a yard on a staged train manually). Then select the staged train you wish this to assume. Check the cars to be on that train and check the locomotives to pull it. Then push "Manually Create Staged Train".
The Manually Add More to Staged Train is if you have selected a staged train from the first tab. You can add more cars to it by selecting from the list of cars.
Any of these extra added cars will either return empty or will be assigned a shipment if one is available. You can go to the Shipments form and create shipments for these cars.