Under the heights tab, the "Bottom" setting determines the depth of cut. The default is to use the depth of the selected contour as the cut depth. But you can offset this, or choose one of the other methods for determining the depth.
There is a ton of useful information here:
Solid Code Solutions | HSMWorks Tips & Tricks
Some of them only apply to the full HSMWorks but many (if not most) apply to HSMXpress also.