You set your tool onto the datum face and zero out as normal, then if the depth of the cut needs to be changed e.g. a step depth is shallow then the tool offset is updated in the length part of the table to reflect the error amount.
So :-
Select tool 1.
Set the offsets table, tool length to Zero for tool 1
Touch the tool onto the datum face.
Zero out the Z DRO
Take a cut of a few thou.
Measure it.
Then adjust the offset length by the error
Remember to make the tool go deeper into the surface, you tell Mach that the tool is shorter.
Graham.