When I measure seat height I usually start at the bottom bracket and the most natural path for the tape measure is up the seat tube centerline and whatever part of the TOP of the saddle it hits is where I do the calculation. Some measure to the top of the pedal surface and that's fine. It takes differences in crank length into account but since you are going to test ride the measurement you took and do further adjustments based on how things feel, I don't think its necessary to measure to pedal surface. The fixed points of BB center and saddle surface are easy to locate and bam, you're good to go.