I measure to where my bones contact the saddle, so either ichial tuberosities or pubic ramus, however you perch on your saddle. There's really not another way. Align the cranks with your tape measure, measuring from the center of the pedal axle to the specified point on the saddle. Which of course only works for transferring saddle height measurement from one bike to another. Initially one can start with a formula or heel-on-pedal and modify by feel.