I have a couple of locations I'd like not to appear in the compass at the top of the screen but when discovered appear on the map. How can I do this? Thanks.

I think you cannot hide "selective" locations from the compass unless you don't modify the swf file.
However you can do this:

Set the map marker initially disabled
Place a defaultenabledisabletrigger volume around the map marker with the linked ref to the map marker.