This is our life, unfortunately, so I have a couple of tips. First, check that the car seats have a sticker showing they are approved for aircraft. One of ours is not and, at least half the time, the airline makes us check it with the luggage. Usually hasn't been a problem in the U.S., but it's good to know ahead of time and be prepared if they don't let the seats on the plane.
Pack as lightly as you can, but bring an extra pair of clothes. For a while, our children, who never have accidents, would always do so on the plane. Either that, or they spill an entire airplane apple juice in their laps.
Both our car seats can roll down the aisle of most planes. So, what we do is load one on top of the other and strap them to a frame with wheels. We use bunji cords, so it isn't elegant, but it gets the job done. But, it sounds like your seats may be large and you know best whether they will fit. There are several companies that make bags and kits for turning your car seat into a backpack. They aren't too expensive. I'm considering it for our next trip.
The worst thing about landing in the middle of the night is waking the sleeping children, removing them from their cozy little nests, lugging them off the plane, walking what seems like miles of corridors, waiting for luggage, etc. You may need to carry both the children off the plane in addition to your seats and bags. Yours may be OK when woken in the middle of the night, but ours usually little wrecks. Be sure you have thought of how you will carry them off the plane and through the airport while they are flopping around screaming and crying to go back to sleep. (sorry, this is what happens to us anyway.)
If you are able to wait until the plane clears, the flight attendants will usually help you carry the car seats off the plane.
This sounds like overkill, but... It doesn't hurt to do a couple of practice runs in your house so that you know how all your stuff fits together and how you can best carry it.
Good luck!!