@Jens, In trying to better explain it, I just confused myself more! LOL. Now that I think of it, it doesn’t matter that the model is centered on the registration pins. Doing it your way (hole through work piece and spoilboard), what IS important is that the registration holes are centered on the work piece. This essentially mimics the method Grant describes. The difficulty you might be having is likely caused by not being able to place the workpiece exactly as the model expects it to be. Any deviation would cause an offset in the flipped carve. Grant’s method essentially eliminates that error.
