If you travel to the place where the waypoint is located type /way, then follow it by the 3 co-ordinates (space has 3 dimensions so needs a vertical waypoint). Follow this with a name to make it easier. Heres an example,
/way 1000 1000 1000 gunboat
Once your waypoint is generated (followed by a system msg), it should appear in your standard waypoint monitor. This can be further edited in the datapad and your options, things like its colour, how many are displayed etc.
Recently they also changed is so that you can set waypoints for areas while your in another area. You can also drag your existing waypoints from your data pad to a mail and send and recieve them with other players.
Edited, Mar 2nd 2008 3:45am by DrGircenstein