I agree, I virtually always use manual focus. If handholding the camera, I generally set the focus to match the basic size that I wish to achieve and then slowly rock back and forth to get the subject in focus. When photographing something like insects that are moving (or may move quickly) this technique works pretty good. My ratio of keepers to throwaways is pretty high.
If I'm photographing something that is stationary, I may use a tripod and longer exposure. In addition, I almost always use a flash for macro photography, even in bright sunlight. Flash allows for smaller f-stops and correspondingly larger depths of field. This also allows some of the photos that might not have been focused perfectly to still turn out well. My most common procedure is to set the lens to manual focus, camera to manual mode, shutter speed to 1/100 s and f-ratio to something between f14 and f22. I then adjust flash exposure compensation or f-ratio after viewing a couple of sample photos.
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