Either the Waypoint command doesn't work like most games or it isn't working at all. Using the command does absolutely nothing, as far as I can tell.
Ships do not currently support waypoints. Omnis do. If this is not the issue, then this could be a bug, in which case you will need to examine this thread (http://knucklecracker.com/forums/index.php?topic=21384.0).
Yeah, doesn't work yet for ships but it is on my list to add.
BTW, apparently, waypoints can't be erased if you change your mind after you establish it; so you can't for instance recall an omni back until all yellow spots are covered.