I prefer to put on my shoes, then get on the bike. Position the heels on the pedals. Now rotate the crank so that the left and right crank arms are parallel to the seat tube. One leg should be fully extended, yet the shoes is still in intimate contact with the pedal. Repeat with the other leg. Now the height is within +/- 1/4" of the sweet spot.
If you have to rock your butt from side to side anytime during the ride, then lower the saddle by 1/4". A change of shoes may also require re-calibration.