With a Canon Rebel XTi and a 500mm - 1000mm f/8 lens, the question isn't really, Should I use Autofocus or Manual Focus but more so Will Autofocus Work At All?

The Rebel series is a consumer grade series - it was never designed for tracking birds in flight, for example.

You've got 9 focus points and, for the life of me, I can't remember or find in the manual what aperture is required to run them. This question has a wealth of knowledge on the subject though: What apertures are required to enable autofocus, including cross-type or high-precision focusing, on Canon DSLR cameras?

To put it bluntly, with an f/8 lens, I'm not sure if any AF point except the center will work for you at all. Perhaps on a very bright day, but I wouldn't expect much from it during golden hours.

At best, you'll have some limited AF functionality or center point only functionality. At worst, you won't have AF at all and will have to manually focus.

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If your subject isn't moving, I'd try using AF first and then go with manual. The problem with manually focusing with a modern day SLR/DSLR is that they don't expect you to - there are no focusing aids built into the camera (like a split screen/microprism). Some newer cameras offer Live View, which may help you out - it won't do well for birds in flight but stationary ones may work out.

For birds in flight, the same holds true - try using the center AF point and AI Servo to track...but realize that you are asking a lot from your camera here...keepers may be few and far between.