The assignments of shipment to cars is done on a per car type per commodity basis. You can make this as simple or as complicated as you want. The simplest is to have basic car types (BX = all boxcars) and one commodity (Anything). The number of possible combinations of car types and commodities increases as the multiplication of car types times commodities. For example, if you have 10 car types and 10 commodities and each car type can carry one of those commodities, that is 100 possible combinations. Add another commodity, and you add 10 more combinations.
Chances are, you will not have every car type carry every commodity, but be aware of the combinations when adding more car types and/or commodities. Where this becomes important is in the number of cars of each car type which can ship a specific commodity. If you do not have enough cars to fulfill a shipment order, then that shipment may not happen.
To get a better perspective of this, in the Edit Layout Data tab of the program under the rolling stock tab you will see a option "Show Number of Types Needed". This will show a grid of commodities across the columns, and car types as rows. Cells contain a double number. For example, for a boxcar that can ship grains you might see something like this in the intersecting cell 16/23. The first number is the number of shipments that need this car type that ships this commodity as per how you've done the shipments. The second number is the number of cars you have assigned to do this commodity that are of this car type. Should the first number be larger than the second, it will show in red. This indicates that you do not have enough cars to fulfill the shipments you have created.
You have two options. The first option is to buy more cars (to add to your already crowded layout), or you can reassign existing cars to ship this commodity. That action will rob other commodities of the proper cars for shipments. Thus a balancing act will be done by you. Ultimately, you may end up just getting more cars.
These limitations are not a result of the program, but of the shipments, commodities and car types you have set up. The program does have this, and other, methods of managing your configuration, but at some point you have to manage things on your own. For example, it is possible that certain shipments will not happen simply because you do not have enough cars of the right commodity. Here is an example.
You have indicated that a shipment will happen daily from a grain elevator located on the dock at Owen Sound (using the demo layout as an example). They require 2 boxcars that can ship grains daily. On that basis alone, there needs to be 10 box cars that can ship grains. Thus if you only have 8 cars assigned, when Friday arrives, no cars will be available to assign to Friday's shipment and it will not be done. (The program does not store pending shipments for later catch up as that would just compound the problem). This may not be a big deal and can be ignored. Eventually, cars would be freed up and the shipment gets done.
Compounding this problem more, in the extreme, is that you indicate that it takes 5 days to fill a car. Thus, on Monday two cars arrive, they have to stay until the following Monday (assuming you run your layout on a 5 day working week), but since there are not enough cars for the previous Friday, no cars will be available for this Monday either. Then the car has to get to it's destination, which could take days, even weeks. Once at it's destination, it takes an additional 5 days to unload. Thus you could easily tie up those 8 cars for two to three weeks, meaning your daily shipments happen for a week, then nothing for 3 more. And guess what, it will be those same 8 cars that run the same shipments again, and again, and again.
This is all because 1) you did not have enough cars of the right commodity in the first place. 2) too many days set to fill and empty cars. Thus, again, it's up to you to balance things out.
Also, keep in mind that some of this is relieved by having secondary commodities assigned to cars. It will help as long as the car with a grain secondary shipment is also not tied up doing it's primary commodity shipment.