I've been meaning to ask for a while about birds in flight actually - as in, which AF scenario to use. I must admit, the 5D3's autofocus options have always rather baffled me - even though it gives examples, I've never known which is most appropriate for birds. I don't do much BIF work, as I'm mostly shooting small songbirds, and not the big owls/eagles that you guys have access to in North America (and other such places). But when I see, say, a duck, crow, or cormorant (i.e. a medium-sized bird) flying, and I try and focus on it, the camera almost never chooses the bird, choosing the sky instead (that being the much larger target). I'm hand holding, and so keeping the AF point on the bird is very hard, but using multiple points or a zone doesn't seem to help. Sorry if all this has been covered before, but I thought I'd ask here anywayFirst of all, a caveat: shooting birds in flight is tough. Even the best gear and technique won't guarantee a good shot, but there are ways to increase your success. The best way to do this is to set up in a stationary location and wait for birds to fly over. It also helps to pre-focus at the distance you expert to acquire the target (BIF). In terms of AF settings, the 7D works best with Zone AF, and the 5DIII and 1D X works best with the the 61-pt auto-select, but it often picks the sky (as you say) if you don't get the BIF with the right initial AF point. The most reliable thing you can do is set it to 61-pt, AI Servo and use the AF Point selection to pick the center AF point. Case 1 seems to work well for me most BIFs, but I'll use Case 2 when there are trees in the way and Case 5 when shooting small birds like swifts. The key is getting the initial AF point on target, holding it until you can verify that it locked, following the target for a moment, and then pressing the shutter. With small distant birds and/or with birds in a gray sky, that can be really tough, but the sooner you are able to lock onto the BIF and start tracking it, the better. If it doesn't lock on, release the AF button and push it again. Sometimes I'll do that 2-3x before it will lock if the BIF is small/distant.
So to recap, set up in a place you expect to see BIFs, lock onto them as soon as you can, confirm focus lock/tracking, wait for key moment, then fire away.
The final key to BIF photos - practice, practice, practice.