I suggest reading the 1DX focusing white paper.The AF system is essentially the same as the 5D3 in terms of setup. It's aimed at sports but you can apply the same principles to birds in flight.
I have played around with the settings on my 5D3 while tracking birds in flight but I'm no expert. I found tracking with a sidekick and my 400mm DO needed different settings to say hand handle panning.
For small birds I would use expanded AF points but shooting albatross I always use single point to focus on the head. With a four metre wing span the AF tends to lock onto the wings if I leave it to it's own devices