Hi fly1937,
after setting uo a free roaming session click on The full screen symbolfor the chart you will then find at the bottom of the screen means of adding waypoints, removing waypoints and an auto pilot system. to understand this go to your main game installation and click on "projects" then "Shipsimulatorextremes" where you will find the manual for the game. pages 20 and 21 explain the use of the system.
Angus