Hi tdomask,
Where the machine origin is shown in the 3D view is where you must set to be the coordinate 0,0,0 on your machine - and you'll likely also want to make sure any kind of work coordinate offsets are disabled as well. If you set the top surface of your canvas to be the project's Z origin then you should be zeroing your machine's Z-axis with the cutter touching the top surface of your workpiece. If there is any kind of tool Z offset this will affect things as well.
Keep us posted!
- Charlie