Hi Captain_Scott,
You can only plot your own course in free-roam, and only within the current environment.
In missions, the “course†is laid out by the creator when he places waypoints. This does not actually define your course, as there may be a big pile of dirt or rock between waypoints.
The green tick on the compass rose points directly at the next waypoint; it is not necessarily the course you should follow to get there.
You can gain some insight into how things work by downloading and studying the Mission Editor tutorial from this post:
http://www.shipsim.com/ShipSimForum/index.php/topic,2886.0.html (http://www.shipsim.com/ShipSimForum/index.php/topic,2886.0.html)
Regards,
Marty