Canon's manual for the 20D - and I presume the 350D as well - is magnificently unclear about focusing modes. I assume that the person responsible has now been promoted into a high-powered position in the public service, or is possibly drafting taxation law. (He would be a natural.)
But the big thing with flight shots is to turn all the focus points on - it is very difficult, perhaps impossible to get the bird exactly on the centre focus point (or any other focus point) and keep it there as it flies over. With a long lens and a fast moving bird (any bird in flight, pretty much, except for one of the hovering kestrels/kites) you are flat out just keeping the birds in frame.
So do that: keep the bird in frame, and let the camera worry about a focus point. My 20D (and your 350D too, I'm sure) will do a remarkably good job of selecting a focus point if you just tell it to pick its own points and go for it - even against detailed backgrounds, quite often. If the camera can't focus on the bird reliably, you probably need to get closer, or else the light is poor. In either case, flight shots are not a realistic proposition.
Oh, and I find it helps to fire in salvos: set the camera to auto-repeat and bang off three or four shots at a time, release the shutter for a moment, then squeeze again (a half press for a moment first if you have an image stabilising lens) and go for another set. It's only electrons: shoot as many as you like.