[jeffy162]

If you manually set a way point, you actually have to go to the waypoint marker on your map (not "close", or "near" the waypoint, but right to it), and you should hear a "DING" and the waypoint should automatically clear then. The HUD arrow will lead you right to the "GoTo" point, so you won't have to guess if you went to (or "close", or "near" to) it.

If you are routing your quests through Carbonite (I don't even have any idea if you can do that, or how it would be done, but I don't know everything there is to know about Carbonite, either), I would imagine you would have to do the same thing.

If you are going to the actual waypoint marker on your map, and you don't hear the sound and the waypoint doesn't automatically clear, then I would imagine the only recourse you have is to right click the map and "Clear Goto" in the menu.