Hi! I've travelled a ton w/ my 3 month old and his bugaboo. I'd recommend NOT checking it until you get to the gate. I usually check one suitcase (clothes, etc.) and his Pack N' Play, and push him to the gate in his stroller. It can be such a long way to walk to the gate, and then again from the gate to baggage claim carrying a car seat and whatever else you have with you! Also, I don't know if you're travelling alone, and this is getting to the nitty gritty, but it's really tough to navigate an airport bathroom on your own with a baby in your arms.
Once you get to the gate, definitely ask if there's an empty seat you can be moved next to so that you can use the carseat during the flight. I've flown 6 times with our guy, and only once has the flight been completely full. It really is a relief to be able to put baby down in a car seat once he's asleep. Twice, we've even had the whole row to ourselves!
The one time we had to check his carseat at the gate, we didn't put it in anything, but you could be prepared w/ a large plastic bag - they fold conveniently in case you don't need to use it.
Good luck and happy travels!