Mike, you could either literally define the stock as your whole stock, and place the geometry where you want the cutting to go.
The easier way that I've used, is to just let MeshCAM "shrink-wrap" the stock to the geometry so X0 Y0 is at the lower (front) left edge of the geometry itself. Then when I set up the machine, I'll zero the X and Y after I've placed the spindle where I want the geometry to be cut. That way, I can throw a random piece of stock on the machine and not worry about X and Y margins, centering, etc. I don't know how big your workpieces are, but for my little ones, I'll print out a full-size outline of the piece to set on the stock and use to position the spindle at X0 Y0.
All opinions in this post are mine alone. I am not a MeshCAM employee, I do not have a financial interest in MeshCAM, nor do I speak for MeshCAM. MeshCAM user since Beta 5 in 2003. viewtopic.php?f=11&t=15333