Ya, just do what Geof said and jog your tool down to the part or your setting fixture. When you get it set at the height you want. Then go to the OFFSET page. Highlight the tool that you are setting and push tool offset measure. If you are using another tool then push next tool and set it the same way.
After you have touched off all of your tools, then add you fixture height if needed. What I mean is that if you used a 4" touch-off gauge to set them, now is the time to add the gauge height to each tool, such as -4.0" and enter.
Keep it simple until you are confident.
Mike
Two Haas VF-2's, Haas HA5C, Haas HRT-9, Hardinge CHNC 1, Bother HS-300 Wire EDM, BobCAD V23, BobCAD V28