To add respond to the post above--you can also change the offset of your Z Zero plate--in the "preferences" tab of the Fire-Up app. the setting there now should be something close to 0.75" which we set when we tested your tool in the factory. That setting simply means that there is 0.75" of space between the top of your Z Zero plate and the bottom of the handibot (the usual location for the top of the material).
If you zero your bit using the z zero plate and then manually move the bit down until it touches the material...the amount that you've "gone negative" in the z axis is the extra amount you need to add to your "z zero plate thickness" to get the right offset for what you're working on.
Does that make sense?