Well, on a body with a laminated top, I actually put the body blank on the machine first, before I glue the top on, and have it engraved a little hash mark at the center, top and bottom (y axis) of the wood. Then I use those lines to line up the top when I glue it on. Since my blank rests in the exact same spot, I don’t have to find a new work zero before I cut the body.
On a solid body, like with a book matched blank, I clamp the blank in and jog over from 0,0 until I get to the center line, keeping careful count of how many mm it is. The I recenter the x-axis of the design to that point