BK, an old system of marking boats - also used on aircraft - is to have stations. They are in 3D, using (1) Waterline reference (use the bottom of the boat as zero, and go up in 1 inch increments. Also (2) Longitudinal. stations, starting at the very front of the boat as zero, and going aft in 1 inch increments. Finally, (3) Gunnel stations starting at centerline and going left and right in 1 inch increments. You can rename these to suit yourself.