The bridge itself for both two and three rail is exactly the same. The way the two rail track bed and the three rail track bed is attached to the bridge is exactly the same. The swap is easily accomplished by turning the bridge over and removing all the small black phillips head screws that hold the track bed to the bridge (they go thru black metal angle brackets).
You don't even have to use the Atlas three rail roadbed. Any track can be placed and attached atop the plastic exposed beams.