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The main problem with using autofocus in macro photography is that a subject moving toward/away from the focus point is one of the harder things for a camera to keep up with. With macro photography if you are hand holding the camera you will have a "breathing" effect in that you will slightly move toward and further away from the subject all the time, unless you've braced yourself against something static like the ground.
As a result AF can have a really hard time keeping up. It doesn't help that many macro lenses tend to have much slower AF drives in general as well.
Canon did actually start to address this with some of their newest lenses - the 100mm IS macro had a hybrid anti-shake system that worked not just in the up/down left/right axis (as most IS do) but also in the back/forward motions as well to give a massive amount of help to the AF systems.
However most lenses do not have this type of hybrid anti-shake system. As a result many macro photographers will use manual focusing; setting the focus to what they want and then moving the camera and lens into range to take the shot. In theory you aren't moving the focus whilst shooting, you adjust it to suit and then focus by moving closer/further away. Basically the same body motion you'll be doing with AF. You then have to learn to gently squeeze the shutter button so that when you press it you don't add shake to the setup as well (something that is important to learn for both auto and manual focusing with regard to macro).
AF systems have come a long way over the years, and more modern cameras are more capable than the old, however in general many macro shooters still prefer to use manual focusing for general shooting. With practice it brings more consistent results because you're not longer having to contend with your own natural swaying when hand shooting; and the AF system at the same time.
If I were shooting with backbutton AF I'd certainly be using the limiter switch on the lens (which I assume you are already doing).; however personally I find it easier to use the manual focusing method outlined above.
As a result AF can have a really hard time keeping up. It doesn't help that many macro lenses tend to have much slower AF drives in general as well.
Canon did actually start to address this with some of their newest lenses - the 100mm IS macro had a hybrid anti-shake system that worked not just in the up/down left/right axis (as most IS do) but also in the back/forward motions as well to give a massive amount of help to the AF systems.
However most lenses do not have this type of hybrid anti-shake system. As a result many macro photographers will use manual focusing; setting the focus to what they want and then moving the camera and lens into range to take the shot. In theory you aren't moving the focus whilst shooting, you adjust it to suit and then focus by moving closer/further away. Basically the same body motion you'll be doing with AF. You then have to learn to gently squeeze the shutter button so that when you press it you don't add shake to the setup as well (something that is important to learn for both auto and manual focusing with regard to macro).
AF systems have come a long way over the years, and more modern cameras are more capable than the old, however in general many macro shooters still prefer to use manual focusing for general shooting. With practice it brings more consistent results because you're not longer having to contend with your own natural swaying when hand shooting; and the AF system at the same time.
If I were shooting with backbutton AF I'd certainly be using the limiter switch on the lens (which I assume you are already doing).; however personally I find it easier to use the manual focusing method outlined above.
