Hi Nate,
You can set where your machine will be zeroed out relative to the canvas volume from the Canvas Properties panel. Any changes to the origin requires recalculating any toolpaths that have already been generated - at least for now but we're planning on changing things so that the origin can be freely moved without recalculating toolpaths or simulation heightmaps. We're just about to release v1.80b soon which includes the ability to set the machine origin outside of the canvas volume as well so that you will not need to create a canvas that's large enough to include the machine origin within its volume.
If you move the machine origin to the top of the canvas then you will want to zero your machine on the top of your work piece, in most cases.
Be sure to do a dry run above your workpiece (zero your machine up in the air) to make sure that it will go through the correct motions when it's actually cutting, just to be safe!
- Charlie