Granted, Mapsource isn't the most intuitive software.
1/ Define your base route by clicking the Route Tool icon (three black dots joined by a red line) and click start and end points
2/ Now press the Esc key on your keyboard and click the Selection icon (white arrow)
3/ Click once on the purple route formed in 1/ above, it will turn yellow which signifies that is the active route
4/ Now click on the route and it binds to your cursor, click somewhere else and the route will change
5/ Repeat as necessary to form the route into what you require
To remove a waypoint added using the above method:
1/ Click off the route to make it inactive (purple)
2/ Click the waypoint you want to remove, it should turn yellow
3/ Right click the waypoint and select delete Waypoint and confirm
There are a few different ways to do the above but that's generally how I do it. HTH.
You can, of course, define the whole route using just the Route Tool clicking each waypoint in turn though you will probably have to either move, delete or add waypoints to get exactly the route you want.
