As a practical matter, while the Atlas trucks now have rotating bearing caps, I don't think you gain that much switching from MTH 3-rail trucks to Atlas 3-rail trucks. Usually this type of discussion is related to 2-rail conversion.
That said, a simple way to mount Atlas trucks to an MTH car is to get a small section of 3/16" wood doweling and mount it into the MTH chassis, then enlarge the hole in the Atlas truck to 3/16" and use the Atlas mounting screw to hold it on the dowel. I've used this trick to fix Atlas cars that had the mounting stud snap.