Having just done a trip with two babies, here's my advise...
Take the car seat for the toddler to sit in. It confines them in a familiar place and at least for my daughter, she fell asleep. We tried having her sit in the seat without the car seat and it was a nightmare.
Pack snacks and juice. You can bring juice, milk and formula (if you use that stuff) for kids if you declare it at the checkpoint. The same thing goes for medications. You can bring all the liquid meds you can carry, but you have to declare it. You just can't carry more than 3oz each of things like toothpaste, makeup, and other toiletries that all have to be in one 1 quart baggie. Bring lots of snacks like apple slices, goldfish, cookies, and other non-messy finger foods. You can't predict when meals/snacks are going to be served and there isn't always time between flights to get something in the terminal. Also, more than likely, the snacks you bring will be familiar and comforting if travel starts to be overwhelming.
Bring a few toys, but bring them out one at a time. If your child like coloring, the wondercolor markers and coloring books are great for no mess play.
Bring at least one change of clothes for you and the child in case of spills or sickness. Especailly with such a long flight, you don't want to be soaked or poopy or wet from vomit for hours. I was very thankful for the extra clothes when my newborn lost her breakfast on me while waiting at the gate for our first leg. 5-6 hours with soaking clothes wouldn't have been a lot of fun.
Ask for help! The flight attendants are your friends and are there to help you. Pre-boarding has its pros and cons. Yes, you can get on the plane before everyone else and the flight attendants have a little more time to assist you, but you're parked in the seats for the amount of time that it takes to get everyone else on board. If your child is a bundle of energy, skip the pre-boarding and hold out as long as you can to let them run it off. If you have to change planes, ask for help in getting from one gate to the next.
If you have a big stroller, take it. I wouldn't have been able to make it through the airport with two babies and the car seat and the carry-on bags by myself otherwise. Most of them have a basket you can stow a few diaper bag size carry-ons. I was able to push the newborn, carry the toddler in a sling, tote the car seat in a bag on my back, and have all the carry-ons ride under in the basket.
Get a bag for the carseat. Babies R Us carries bags with wheels and carry straps for transport through the airport that run between $30 and $40. The one I have reverses into a sun shade for the seat so it won't overheat in a car. It was one piece of kid gear that I recommend to any parent that travels by plane.
I hope this helps on your trip that is going to much longer than the one I just took. If you have another adult going with you, switch off kid watching duties so that you both have a chance to be somewhat rested.