Do you use photoshop CS5 or 5.5? I shoot product photography a good chunk of my time (what pays most my bills)... I do focus bracketing...
Not to muck with a successful workflow, but have you considered Helicon Focus?
I have tried and bought helicon focus a few months ago, whilst it is good, you do need to fix some mistakes, and a rack for the camera would help the little size diffrences caused by refocusing.
Auto bracketing? is that a camera option i missed?
and yes i am a ps5 fan :-)
There's no auto focus bracketing... I do mine manually (usually around 2-8 shots depending on how macro I've got to get my lens, and how physically big it is... ) I do like in photoshop CS5 it keeps all the layers and keeps the layer masks so you can just use your white/black brushes in the layer masks to reveal and hide areas it may have missed... In the end it's a computer guessing what it thinks is sharp in relation to other files in the same area and if you have decent ram and processing power, doesn't take that long. Quick hint, if you want to play with it, use photo merge... use auto... it usually does a good job... and unclick blend images... if you dont unclick it will think it's a panorama and royally screw things up, but once it aligns it, use autoblend and that will create the stacked image and masks...
Unfocused... in order to understand DOF better, there are tons of DOF calculators like neuro suggested... They also with any lens, a 50mm or 400mm, the closer your subjects are to your lens (minimum focus distance) the shallower your DOF will be and farther away in relation to what your lens focuses (wider lenses can reach infinity near 10-15 feet while tele's may go 40-50 meters if not more... ) Using that focus scale as a rough estimate, using your aperture to your advantage, and looking at DOF calculators if in doubt, keep in mind if you're using crop or FF, you will have greater control over bokeh and or large DOF.