Yep, working out the details on this myself. However, I'm using Fusion 360.
On my fixture soft-jaw, I machined in a .25" x .25" x .125" deep indicator box so that the soft jaws can easily be set up and aligned. Working out the details on how best to do this in the CAM section based on probing for location where the parts "actually" end up when in the fixture.
http://www.cnczone.com/forums/tormac...980-g59-p.html