The method for centring a probe in a mill is to use a conventional DTI touching the probe ball and rotate the spindle manually. Then adjust the 3 screws so you end up with no runout on the DTI when you rotate the spindle. Which 3 screws to adjust depends on the probe. On my Renishaw (ebay purchase), they cause the body to pivot about a ball bearing. It's trial and error and a bit of skill, rather like setting up a 4-jaw chuck but not difficult at all.

If you plan to rely on software settings, you will need to ensure the spindle is always at the same angular position each time. Setting up the probe as described is pretty straightforward and I wouldn't go back to an edge finder now.