1) Set unit on map (nicknamed TheDude).
2) Place 5 waypoints on editor map (WP1, WP2, WP3, WP4, WP5). If you're trying to make waypoints in-game rather than in-editor, that's different.
3) Make a script:
_randomArray = [WP2, WP3];
//Presumably, WP2 and WP3 are variables for arrays like [(group TheDude), 3] and [(group TheDude), 4]
_randomSelect = (_randomArray select (round (random 1)));
// This will select either WP2 OR WP3 randomly
deleteWaypoint _randomSelect;
//This deletes the selected waypoint, leaving the other one as the only option
This way you can predefine the position of each waypoint via the editor while also randomly choosing one of the two waypoints (by deleting one). I hope that helps (though I might have misunderstood you).