One huge challenge for Nature photographers is to capture birds in flight.
A lot of it is luck because to some extent you have to have the birds play the game before you can get the shot.
That being said you can create the best possible scenario for you to have the best advantage.
If possible I prefer to have the sun at my back, or over my shoulder. This makes for a real nice photo because the wings spread highlighted feathers have a great look, especially on white birds.
Obviously you want to use a fast shutter speed to stop the action.
I think the hardest part of the whole shoot is getting the focus right.
This is where if you talk to ten wildlife photographers you might get ten answers.
I really believe it boils down to what works with the camera you have in hand.
Experiment with them all. I have tried manual focus to try and let the birds fly into the focus plane.
I tried auto focus hoping to get it before the lens changes again.
But the method I have had the most luck with is to have the camera on auto focus, but to press the shutter halfway on a bird flying. This kind of locks in the close area so you don't have to guess at the distance like you would in manual focus.
And when the birds look right push the shutter completley down to get the shot. This works many times and prevents the focus from moving in and out continuiously.
And of course take many shots and hope and pray that at least one did what you wanted.