Just go up to the CM at the entry to the ride and tell them you need to do a baby swap. We traveled last November, and one of our children was not tall enough for the "big rides". Many rides are different as to exactly where you wait, but the process is essentially the same. One parent (and any other family members who are riding) enters the line (we used the fast pass system and so always went in the fast pass line, but certainly you can use the stand-by line) and tells the CM they need to do a baby swap. The CM will give you a little piece of paper and writes something on it, which you keep until the end of the ride. The other parent waits in the designated location. First parent rides with family and then meets with second parent (who's been waiting with little one). Second parent then takes that little piece of paper back to the CM who is at the entrance to the fastpass or stand-by line, and the second parent is allowed to take up to two more members of the family. Go right back up to the front of the line. This was great, because my bigger kids could then ride the attraction immediately again.
At BTMR, the second parent (with child) waits at the entrance of the ride, but on Primeval Whirl, the second parent (with child) waits in a fenced in area within the attraction. So it really depends on the ride.
Good luck, and have a great time!!