aren't you using a bridge camera? (So no extension tubes?)
I use autofocus with close-up lenses on bridge cameras and on telezoom lenses on micro four thirds cameras and a dSLR. I use autofocus with an Olympus 60mm macro on micro four thirds (without extension tubes or close-up lenses).
I just tried various combinations of kit with extension tubes, hand-held, using a variety of subjects. with scene sizes of around an inch and a half to half an inch across (around 1:1.5 to 2:1 in APS-C terms). Working distances were very short compared to what I am used to, as little as a centimetre, perhaps less, for some of the test shots (In fact with the zoom lenses the working distance went to zero as focal length reduced (giving a nice picture of the dust on the front of the lens) and then negative (focusing inside the lens). Only a small range of focal lengths with the zoom lenses gave positive working distances.
Although a bit slower at times than with my usual setups, autofocus seemed usable to me with the following combinations, using live view (which is what I normally use).
Canon 70D (APS-C) with 18-55 and 36mm extension tubes
70D with 18-55, 68mm extension tubes
Panasonic G3 (Micro four thirds) with 12-60, 26mm extension tubes
G3 with 14-42, 26mm extension tubes
G3 with 45-200 , 26mm extension tubes
G3 with 60mm macro, 26mm extension tubes
There are some examples from the 70D test shots in
this album at Flickr, all except the first using the 18-55, some with 36mm extension tubes and some with 68mm extenstion tubes. The first was with the Sigma 105 with 68mm extension tubes.
Phase detect autofocus (i.e. using the optical viewfinder) hardly worked at all with the 70D, so much so that it seemed totally unusable to me.
Because of extensive hunting the Sigma 105 macro on the 70D with 68mm extension tubes seemed unusable to me with live view as well as with the optical viewfinder. (I get a lot of hunting with it even without extension tubes, which is one of the reasons I don't use it other than for testing/comparison purposes like this.)