My suggestion is get a good quality backpack which is big enough to hold everything, plus some camera inserts (like F-Stop ICUs, Mountain Smith Kit Cube, etc), plus a good day pack. Might be handy if the day pack was a camera pack which allowed quick access to a camera compartment - maybe something like a Lowepro Photo Sport bag, but that might not be large enough for you.
Anyway, when you're on foot, everything goes in the packs and your hands are free. Ideally there would be a way to securely attach the day pack to the large backpack so you can make use of the room in both packs when carrying everything, but otherwise you'd just have to fold up the day pack and put it in the large pack. And obviously when you've got a base to leave things and you're doing short trips, just take what you need in the day pack.
On flights, camera gear goes in the day pack and that's your carry on baggage. If it won't fit, you might get away with carrying one of the camera inserts as separate item, along with the pack(?).
My belief is there are very few camera packs which are even close to good enough as backpacks to be comfortable carrying a fairly heavy load for very long. For camera backpacks, I have a Lowepro Fastpack 350 which is not good for carrying a heavy load for very long, and a Lowepro Rover Pro 45L which is reasonable. Some of the newer Lowepro bags may be OK (not sure), and I've heard good things about the F-Stop bags. But if I was going on the sort of trip you're talking about, I'd definitely go for a good quality hiking or travel pack and add camera inserts.
