I've discovered something.
Opa discribes in one of his tricks & tips about going to map mode and dragging the aircraft icon to change the location. The same can be done with the tower and you can pinpoint the location by lattitude/longitude and altitude. Unfortunately it only re-locates it for that flight.
For Seattle-Tacoma for instance I flew the aircraft directly over the tower, paused, went to map and dragged the tower icon to the aircraft icon and it worked.
Can anyone suggest a way to perminently save the tower location?
I sometimes create a flight, move the tower and increase its altitude as stated here. I then save the flight as "parked at......". When I need to create a new flight from that airport, I open the saved version and make whatever changes I need, (aircraft, flight plan etc.). Not too involved as long as you don't fly from too many airports.