Have you tried looking through the eye piece with your right eye while keeping your left eye open? If you haven't shot like this with a telephoto then I suggest you first try it while sitting down, as some people can find it very disorienting. (I learned this the hard way when I was showing a friend how I use my gear. She nearly dropped my 7D with the 150-500 lens, and then barely missed my shoes when she puked.)
The way I sight birds in flight is to start by setting the focus for the lens roughly where I'm expecting the subject to be. (Using trees or bushes roughly a similar distance.)
I then begin sighting over the top of my camera to start tracking/panning with the subject. Then I'll keep both eyes open and put my right eye to the eye piece while still keeping the camera in motion. Usually the subject will then be somewhere in the frame, and I can adjust slightly to get the centre point on one of them and start focus tracking, but if not I can do larger adjustments while watching the bird out of my left eye.
I find gulls tend to make fairly nice test subjects for this kind of thing. They're easily found in large numbers, and are generally fairly active with a mix of smooth and erratic motion to keep you on your toes. They might not be as interesting to photograph as eagles or hawks, but you can pack in a lot more training in an hour of shooting with boring old gulls than you can with pretty much any other bird.
