Try opening the airport in X-plane, click on location - local map on the toolbar at the top.
click "edit" on top of this screen, then click on the "GS" box that you want to move.
change it's location by adjusting the latitude and longitude settings on the left side.
When you have it where you want it, click on the "GS" box again to un-check it, then click on "edit" again to quit making your adjustments.
When you shut down X-plane, it will ask if you want to save your changes to NAVAID. Click "yes" and it will save your moves.
I hope this helps... also check out
http://forums.x-plane.org/index.php?app=downloads&showfile=19201
Matt