Lyman,
The best thing to do in calibrating is clamp your brake at each end and don't let go of it when you turn around. This way you're essentially making one continuous measurement of all 4 (or more) rides. Divide the total counts by the number of rides, and whether you misjudge by a part of a count isn't really as important. Of course you should still record the counts at each stop because you want to make sure the rides are consistent.
For more precision I used to number my spokes, and you can estimate to the nearest 0.1 of a spoke interval, ~0.5 cm or 0.25" for a 36-spoke wheel. In fact you can use spokes only with no loss of accuracy. AND with a little concentration you can remember all the intermediate spoke readings and avoid doing any writing between start and end of calibration.
I'm sure that is "illegal" so let's just say I'm speculating that this could be done :-).
If you're thinking about trying electronic measurement with a protege it may be more convenient to number decimal parts of the entire wheel circumference rather than spokes.