Make a location over the whole MAIN area that the bunkers will be built in. Then you can use either the Supply Depot area [A spot on the map with TONS of supply depots], or you can use the Norad II method [A bunch of prestacked Norad II's {Saves space}]
Now, for the trigger:
When a bunker is detected in the MAIN area, have a location centered on it the size of the bunker. Have it create and enter any units you'd like. Then REMOVE 1 of the Norad II's, or Supply Depots [If using supply depots, have a location center on supply depot with preserve trigger], and use the teleport {move} trigger to put it where the removed Norad II or Supply Depot was.
Basically, this will make it only detect where you want it to be built.
If you don't want to use the MAIN area triggers, you could add in giving the bunker to a computer ally player along with the teleport {move} trigger.