I think that depends very much on the ride. Most Disney rides with parent swap don't have the unload and load areas in the same place. When we did a parent swap at Rock n Roller Coaster, my wife waited outside and then went through the fast pass line after I returned. You might be able to do a parent swap by going through the line together, and then one of you taking the 'chicken out' exit before getting on the ride.
The problem is that if your child doesn't meet the height for the ride, the first CM at the entrance to the queue might not let them pass....I seem to remember that the unofficial guide to Disney World has a section on parent swapping for more info too...