The convoy will go on a schedule from one point to another. The way it will go is caclulated at the start and never changed until it arrives or the way is blocked.
If a waypoint is in a station, then you will see the station name as a schedule entry, otherwise just waypoint will be written. Waypoint means, that at this point the convoi calculates the route to its next entry in the schedule.
If you have more than one level e.g. monorail and normal track one over the other, you can use the CONTROL key to determine which level you mean. Using (ctrl) + click will add a waypoint above ground level, where just clicking on it will add a waypoint at ground level.
Line Management window.
When a convoy is assigned to a line, any update made to the line will be applied to all the convoys on that line. Any change made to one of the individual convoy's schedule will only affect that convoy.
Remember: Every vehicle has it's own schedule. A line is a template like schedule that can be applied to multiple convoys. Changes to the line affect all convoy schedule's on the line.