The track marks are for AI (computer) drivers to follow. You, the user, presses the number 1 key on the top of the main part of your keyboard and climbs in. You may want to go ahead and flip the switches for yourself ahead of time to give you a high ball all the way, otherwise, you'll have to stop and flip switches which you can do from within the cab by pressing the J-key.
To hide the switch-levers while in Driver, press CTRL+H so you don't have the bright green and red arrows all over the place.
A variation of this is to go for a ride along with the AI. Setup your schedule as you said, track mark 1, track mark 2, Drive To (station/industry)-platform, Load, etc. and then press the 1-key to climb in the cab along with the AI. I do this often just to go for a ride.