The CM's are usually very helpful regarding the swap. The rules for each ride are a little different; some rides have the whole party wait in line together, and then have an area to "swap" the little ones on the side (Space MT, Star Tours, etc.). Others, like Big Thunder Mt, make one person wait in line, and then once they've ridden, the other person can go in the back. Just ask the CM at the front of the line for that ride, and they'll help you out.
Enjoy your trip!
Wade