In the ship list is an object called waypoint (last one in the list). Place it like any other ship. It will be visually visible in-game. In FRED it will be represented by a purple dot/ball/sphere.
To create waypointpaths, make sure you have a previously created waypoint activated/selected. When you have previously created waypoint selected, and purple line will connect it to the new waypoint indicating they belong in to the same group and any ship assigned to those waypoints will fly them in sequence. To create a single waypoint, or another path, make sure you have nothing selected/activated, and place a waypoint.
NOTE: There is also an object called Nav buoy (or nav point, or nav something). Do not confuse this to the waypoint system. The object is simply a model created by TBP team to be used as a visible artifact in game. For example if player needs to be directed in to certain area or waypoint. Think it as a ship that looks like a rotating letter.