The method varies, depending on whether or not you use FastPass (I'd recommend that you do, so that you are not killing quite so much time with baby waiting for others to come out of the ride.)
With FP, on rides where both kids are too little: Get *one* FP for the ride. When the FP ride time comes up, all of you go to the FP Return line, and ask for a Child Swap pass. One person uses the original FP to ride, while the other waits out with the kids. When the first adult comes out of the ride (you don't have to wait right at the exit; you can take the littles to another attraction if you want, and it's a good idea to do so), then the second adult uses the child swap pass to enter the ride via the FP line. This strategy frees up your additional tickets to be used to immediately get a FP for a different height-restricted ride. That is a big benefit, as normally you cannot get FP for another ride until the time for the first one comes up, but if you have a ticket that wasn't used to get a FP the first time, you can use it for something else right away. If you have a 5 yo, you can use his ticket to obtain a 3rd simultaneous FP for a ride above his height.
With FP, on rides where one child is old enough to ride with a parent: Go ahead and get two FP, then proceed as above. The entire family must go to the FP return gate when the time comes up, to pick up the child swap pass. Then the "babysitter" parent stays outside while the other parent and older child use FP to enter the ride. When they come out, then you leave the younger child with the other parent, and take the older child onto the ride a second time, using the Child Swap pass to enter via the FP line. One Child Swap pass is good for up to 4 riders at a time, and they do not have any time restrictions re: how soon you have to return.
Without FP: Proceed as above, only the entire family must go to the Standby Line entrance to ask for the Child Swap pass. The eligible family member(s) use the standby line to access the ride, while the others wait outside, doing whatever. When the original set of riders come back out, the other parent, along with up to 3 old-enough-to-ride other party members then may access the ride via the FP entrance.
Take your cell phones, and use text messaging to let the person riding know where you have gone. Don't just stand around waiting near the entrance, especially if the first rider(s) are going standby, because you could easily be waiting for 90 minutes or so. Voice mail is generally NOT the best choice; the ambient noise in the park is quite loud, and you'll have difficulty hearing it.
As with FP, you don't have to use the Child Swap pass right away, just sometime that day. You can hoard them and use them one after the other later in the day if you like.