As a keen wildlife shooter and especially keen on birds in flight I use the same routine for a bird in flight. No matter what lens I'm using in both situations I always try and achieve between f5 and f11 I will use shutter speeds anywhere between 1/800 and 1/2000. I learnt my basic skills by taking a half day course at a birds of prey centre. The rest on here at the wildlife forums and then via articles on the web.
As an example look at the two different styles of bird shots below. The first was a slow panning shot of a Shellduck, the second a fast moving follow and click.