i think as long as your measurement is measured from the same point of reference between the 2 pulleys, it could be on the top of the groove, or at the bottom. Just as long as it is consistent between both of them.
then it is just a math ratio thing. i have been using the link http://www.blocklayer.com/pulley-belteng.aspx
to play around with the diameters of the pulleys to see what could work for me.
i have also found a stanley 33-115 circumference tape helps out a lot. used it when i was measuring the diameter of the rope starter pulley. so i could get the exact diameter to calculate for the timing marks.
good luck