Hi @GIban671,
This exact topic (and video) has been discussed in detail in this thread, you may find it useful.
You don’t need to mess with negative thickness values, setting zero to the wasteboard (“bottom” in CC setup) just means that you will have to do the zeroing (with a paper or probe) on the wasteboard surface, not on the material, but the rest is taken care of by the CAD tool that takes the declared material thickness into account to figure out where is the top, how high to retract, etc…