Real simple solution
set your tools off a vise or a location surface, use your fixture offsets to move the tools to the height you want.
for example lets say you cut your vise jaws.
Set every tool off your vise jaws.
when you still a part that is 1.0 tall change your fixture offset to 1.0
when you put the next part in thats 3.0 off the vise jaws change your fixture offset to 3.0
the top of your part in both cases will be Z 0.0
if you take off the vise alot set the tools off the table
i have a rotary table as one fixture height offset 2 vises as another, a chuck as another etc etc.
just dont forget to move the whole fiture offset if you want your tools lower or higher.