Hello Apple266,
In Shipsim, a waypoint is in fact the child of a specific player ship, the parent.
It means just that, you have to begin with selecting first at least one ship before you can create a WP. Having done that, you may create WPs, but you will have to join them to a ship...
First the ship1, then WP1 (->ship1), then WP2 (->ship1), ....
Good luck
Luc