There's prob an easier way.. But, in the waaypoints activation field (In advanced mode) put :
unitnametomove move [getpos gotopos]
Then, put a invisible H (Under empty>objets, I think), can call it gotopos (Change it to what you want, but update the waypoints code where it says getpos gotopos and change the gotopos bit)..
Hmm, you could give the unit you want to move a set of waypoints, but for the first one, make it fairly close, to the unit, and press F5 (Syncronise mode), and drag a line between the waypoint that you need to get to, to the units first waypoint.. I'm not too sure about how effective this is, though...
Hope this answers you prob
- Ben