Starwire,
There are a number of different approaches to resolving this issue and everyone has their own preferences. Unless I am misunderstanding your question, the tool zero position relating to the work has to be set manually or with a probe - from then on zero is zero so to speak.
Just as an example, this is the way I do it
http://www.cooperman.talktalk.net/files/17.htmHope this helps,
Tweakie.