Easy: Do the drive to command. Let the train roll. Open the menu and set the Stop train command. When you get to where you want to go. Do a continue schedule. Problem with this is that let's say you have a 5 mile route, you do the drive (or navigate) to, train rolls and it does not throw all the switches from here to there at the same time: They get switched as the train get's closer to them. But you get to throw the switches manually as you get near in manual mode. Let me sumarize here the 4 commands to make the train go somewhere in AI:
Drive to: Train goes to an industry, station or place similar to that using the "direct way" (It may wait until an obstruction is clear).
Navigate to: It goes same as above but if it finds an obstruction, looks for a suitable way to go through or around.
Drive to trackmak: Same as Drive to (as above).
Navigate to trackmark: As Navigate to.
I know you all know this, but believe me, there is always somebody that can use the explanations.