This page describes how to configure the routes and trains in your layout. The routes data entry is discussed separately, this here is more of examples how to set up different route configurations. Make sure you also check the demo described here to see how those routes are set up.
Here is a maximum layout setup that uses all possible route configurations.
Each town is represented by letters of the alphabet, each route is numbered.
Basically, a route is a series of towns that, in railroad terms, would be considered a subdivision with the first town at mile zero. There are three basic route types. A normal route is one that starts at Town A and ends at Town F. There is also a looped route from A to G to H and ends at A again. The default yard is in TownA. TownF is considered a staging yard for this example and is one of the places shipments get on and off the layout.
Then there are the branch lines. There are three branch lines on this example. Note that one starts at the default yard (B1), while the other is off from the junction town of D (B2) and one (B3) that runs from C (another junction). One of these branch lines (X) has an interchange with another layout and is another portal to the outside world.
The differences between these routes will become apparent when we set up our trains.
Thus this example has 5 routes defined. One from A to F, one from A which loops back to A, one branch from A to X, one from C to Y and one from D to Z. The demo is similar to this.
You do not create a route for the opposite directions (say from F to A), as that is what a train does, not a route. Just think of routes as following increasing mile posts. We will, however, deviate from that a bit to get some specialty trains to run. Just remember that trains can run on one route only, as many as you need. Trains never traverse across more than one route.
Let's throw a twist in this by having a unit gravel train that runs from the staging yard at F to the sand pit at G. This crosses two routes. The solution is to make a route just for the gravel train. Thus you can use routes as true subdivisions if you want or you can use routes to make any configuration that will get trains running where you want.
The next step after creating routes is to create the trains that run those routes, and at this point only consider freight trains. We will concentrate on the philosophy of creating trains with examples. In this example, we have one train that runs from A to E (Train1), one that runs from E to A (Train2). This is a way freight that services all the towns on the route. In this case these are two separate trains that meet at C, one going up, the other coming back down the route. The difference between these two is that Train2 obviously runs the route in reverse direction. You have an option on entering trains to indicate that this train runs it's route in reverse direction.
Trains into staging yards are a bit different. A train that enters a staging yard must reappear again as a separate train designation, but is in fact the same train. You will not be able to run the staging out train until the corresponding inbound staging goes in first. This would be Train3 and Train4. The program knows this is a train going into a staging yard and will prompt you accordingly.
Train5 runs the loop. This train also drops off cars at the towns in this loop. It runs only in that direction, there is no other in the reverse (in this example). There are three branch line trains. TrainM1/M2 runs from Y to C. The route is designated as C to Y, thus this train runs in reverse of that. The other thing about this train is it is an up then back on the same trip. Thus the designation of the train is M1/M2, one train, two designations (but you can do what ever you want). Down to C as M1, then back up to Y as M2. But it is one train as far as the program is concerned. TrainM3 and Train M4 are different. They are two separate trains. When M3 runs from A to X, M4 is running from X to A. Both meet at the junction B. The last branch from E to Z is also an up then back but starting at E, the bottom of the route.
Thus if you have not figured it out there would have to be yards at the following places. A (the default yard), Z (the staging yard), E for cars going up route B3 to be stored for TrainM5 to pick up. There needs to be a yard at C for the branch line train M1/M2 to pick up and drop off cars. There would also have to be at least the following engine storage facilities: A at the default yard, X at the end of branch B1, Y at the end of branch B2 and E.
There are some deviations, or alternative uses for these route concepts. For example, you have a large town that has a local switcher that picks up cars from other trains and disseminates them around the industries in that town. You could make that one town a branch line.
This should give you some idea as to how to configure the system to run your layout. There have been many different designs of layouts as there are modelers, so it is possible that you will have a completely different configuration. The on line discussion site will allow you to bounce ideas off other people as well as this program's developer.