In my CAM software I define the top surface of the work as work coordinates Z Zero. Any cuts down into the work are then in the -ve Z direction. So it goes below zero when cutting but that is normal. Is that what you mean?
You can also define the bottom of the workpiece as zero in CAM and then set work Z zero at the bottom of the work (eg the spoil board). Then all cutting is +ve Z

Can you write down each step you are taking as this might help understand your problem? Explain at which point it does something unexpected. Video and screenshots may help if it is difficult to describe