When you enter the AF finetuning menu you can click on either apply to "all" or apply to "one." You probably want to choose to apply to just one and it will remember the adjustment for each separate lens. I have done this for all my lens and the results match pretty well my other testing methods but this is much easier and faster. Concerning zoom lens, like another poster stated you will probably have to compromise between the focal lengths.
One other thing to watch. I recently just purchased the DA *55 1.4 from B&H and I checked the lens using the Dot Tune method several times and got the same results of -3. Then for the fun of it I checked the lens again at more than double the distance to the target and came up with a +3 results. I sent this lens back for an exchange and the checked the second lens the same way, and the results were within two points of each other so I split the difference and will keep this lens.
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