To get the times correctly you have run the scenario and jot the times down. In your railworks\manuals\en folder in a pdf file called something like TS or Railworks Time Tableview Web.pdf. It will explain how to make scenario. I also made a video tutorial that is in the Learning Cnter on thw eb site here.
So for your pathing question, the editor will make the paths as you choose which stations you want to stop at. If you do not like the way the route is laid out to the stations, you can adjust it by adding markers and then choosing the markers in between the stations choices.
Your best best is to look through the manual I pointed out and then look at the videos online here. Then come back here with questions. Be glad to help you further.