I just started to use extension tubes and one of my flickr friends, Wink http://www.flickr.com/photos/68842954@N00, gave me some very good advice.
Set the camera to aperture to f/5.6 - f/9, manual focus, and the shutter release to continuous, hold the shutter button down as you gently move the camera in and out for a least 6-8 shots for each scene, you can then choose the best focus later.
I have yet to try this out, but I did do several shots stopping up...if you don't you cannot see much. Now I will try it on a different lens. Do not try it on a 50mm...it is too hard to manually focus. An 18-55mm works well and most photographers have that lens in their kit.