>I was taught that once focused on a spot, abut 1/3 of the area >in front of and 2/3 behind the focused spot would be the depth >of field. But I don't see people setting up their focus points >that way and not sure if it is taken into consideration into >the software programs. But I will admit this would be critical >for only some situtaions.
The assumption is that while there is a DOF that people tend to think of as "in focus", that the midway point you mention is more-sharp than other areas in that DOF range, and so by locating it the asymmetrical DOF just follows along. So I'd suggest in FoCal your question is handled automatically because it doesn't look at the DOF range, but seeks the critical best focus at a single distance.
In manual adjustments with something like Lens Align that's a bit different, as I think people by eye are seeing the whole DOF range and estimating the mid-point. So in a real sense you are watching the DOF "bubble" of Focus, and moving the fine tune amount until you like where the bubble appears on the ruler. If one doesn't position it so that more is behind than in front, then you aren't really at the best AF value. Of course with a very fast lens this distance is so thin as not to matter much.
>>I have an 85mm f/1.4 lens that I know is off and >>was kind of tired of dealing with it....
I feel your pain -- I just switch back and forth whether I'm using for portraits or sports, it's a real pain. I'm thinking of sending it to Nikon and see if they can address, but I suspect it's the nature of that lens. Add in a bit of focus shift and there's just no right answer for it.