Kak,
It's not complicated, instead of starting at the top surface and using negative coordinates, you simply start at the bottom and all coordinates are positive, which is actually more intuitive, in my experience.
'Zero' is used as a noun and also as a verb in machining, so those darn semantics get in the way again . . i.e. 'zeroing' (verb) is just a term used for the process of telling the CNC machine where stuff is and it does not necessarily involve the number zero (noun) at all.
Example: Let's say your stock is .75" . . grab your PC board and do the the tool height thing with the Himy stuff and what do you have? You have the end of the tool .75" (material thickness) plus .125" (the PC board) above the bottom of the stock. All you need to do is tell Mach3 where the tool currently is. There is no rule that says you MUST get the tool to 0.000 and then tell Mach it is at 0.0000. Mach just needs to know the coordinate of the CURRENT position and it will know where everything else it from there.
In the example, if you want the bottom of the material to be zero, then the tool is currently sitting .875" above that, so you simply tell Mach where it is by typing positive .875 in the DRO and your good to go. You do not have to have the tool physically at zero on any axis. 'Zero' (the noun) is simply a reference plane from which the coordinates are all taken. It could be on the roof or 100 feet underground.The only caveat is to remember that you physically hit something at positive .875 in our example, so don't get absent minder (like me) and pick up the tool to say .5" for a rapid move or