This is an image of the starboard rear strut of the Shuttle Carrier Aircraft (a modified Boeing 747). If you look closely, you can see the following words:
Nope they were prepareing it for a rescue mission after they saw the foam insulation had hit Discovery. I think they just keep one in rotation and the other one Atlantis as a stand by. I think it's too expensive to have both of them ready to lunch at the same time.