For the Nikon I would recommend getting Control My Nikon.
It has some very useful focusing controls including automated focus stacking.
Very nice software and inexpensive. You could still go through Capture One for
your image processing and viewing if you want.http://www.controlmynikon.com/
It's only $30 so even if you only use it for focus stacking it's worth it.
Also live view is cleaner for some reason at fully zoomed out live view.
The focusing o control my nikon stays put from shot to shot until you tell it to refocus.
You can download a free 30 day demo. However it is PC only for now. Mac version is in the works.