Well, it kinda depends on the ride. First, get FP's for all members of your party w/tickets. Then, most of the time you tell the CM at the front entrance that you need a baby swap pass - usually they verify who the "baby" is, and hand out a pass that is good for up to 3 people. The people who want to ride first then get to ride at the FP time. Afterwards, you can go w/up to 2 more people. Sometimes you tell the CM at the END of the ride that you need to do a baby swap and you can then do it immediately after the ride and not stand in line at all. This happened to us at the Star Wars ride. Unfortunately, it seemed that on a few rides the CM's were not really sure of the procedure. We had some confusion on a few rides - including Test Track, but don't worry - it will work out and you will have a blast! My older kids LOVED riding everything twice!
HTH! Good luck!