Thanks for asking this question - as I have been meaning to. Have been trying to take photos of birds in flight with my humble A200 and Tamron 55-200mm and been having a lot of trouble!
Decisions such as shutter vs aperture priority also come up. But with focusing, should I spot focus or another setting etc.? Also general techniques for tracking the birds etc.
I've been using aperture priority, set to widest, then setting the ISO so that I know I can get a shutter speed of 1/640 or more. Then I use spot focusing and try to get in a position to get birds flying along a stretch of sky (so nothing will be behind) long enough to track, get focus and get some shots off. Of course the birds are never very helpful and so far my results are shocking!
Any tips for these types of questions?