Which camera are you using, and which AF mode? How do you tell when it's locked on? Surely you'd have the same trouble I would have telling whether I've focused on the bird accurately.
I have an E-520 plus the 70-300mm plus EC-14. I use S-AF (single Auto-Focus), and spot-metering. All those pictures I posted above were tripod-mounted, without IS.
You can tell when the bird is in focus because the focus-light lights up when you half-depress the shutter. And you can tell that the BIRD is in focus instead of the branches by what you see in the viewfinder.
If the branches are in focus, you can aim at ANY point on the bird that is revealed and half-press again, and keep doing this until you see that the bird is in focus. Once you have attained focus, as long as you continue aiming at a part of the bird, it will usually continue to focus on the bird on each shot.
Sometimes, especially when you are aiming at a new bird, the focus will get really screwed up and focus on some branches that are MUCH too close, or even worse, the focus will go all the way out and then all the way back and never lock onto anything good. But to solve this, you can just pick a fairly well-revealed branch NEAR the bird and focus on that. Then, once you are in the correct area, aim at any point on the bird and half-depress.
I am spelling this out very carefully, but in practice it happens pretty quickly, moving the focus point to the bird, and firing. Once the focus is in the approximate area and you aim at the bird, the focus is instantaneous and you can see it happen.
Of course, if the bird is really moving fast, you don't even bother with the half-press but just press the whole amount on each shot. When you are doing this, you can tell if you have lost focus by what you are seeing and just use half-depress again to get yourself back on track.
As far as whether the bird is focused properly (i.e. exactly in focus), this is not much of a concern with auto-focus. If you are aiming at a part of the bird and the focus light lights, generally speaking the focus will be exactly correct. It's extrememly fast. Of course, if you are close, there are concerns about depth-of-field, which can be a problem if you are focuing say on the bird's chest and he is facing you and therefore his beak is closer.
I think that this is one of the BIG differences between using auto-focus and manual focus. With MF, even when you think you are in focus perfectly, often you are not (unless you have a ton of time and can use the 7x or 10x zoom view). With AF, you can be pretty sure the focus will be perfect when the focus light lights.