I have been cncing guitar parts for about 15 years now. I make the bottom of the centerline my X0 and Y0. That way I have a glue joint or a centered pencil line for bodies when flipping them over. For necks, I always cut the truss rod first in the neck wood. I have a matching slot with a strip that I use on the table. Think of a keyway and key in a shaft, and how that fits. That indexs the neck on center. I use the X0Y0 at the bottom of the neck too. Because the Xcarve has a tendency to shift during a tool change, I home if after each bit is installed and then rezero. I use a Dremel pointed burr to rezero on the mark. I’ve tried dowels and find them less than satisfactory for the accuracy I’m trying to achieve. This is a auxiliary board that is double sided duct taped down and leveled before I start carving the necks. You can see a groove the width of a skunk stripe is machined into it.
This is ready for the stick that fits into the groove to do the fretboard side.
This is my Dremel burr used to locate the point for 0,0. I use it in an adaptor for 1/4" bits.