-- Last Updated: Jan-30-13 4:40 PM EST --
If one really cared you may need to do say a one mile course ten times alternating between using the skeg and not. Be careful you don't make wind direction skew your results. Your speed would vary each lap but if the difference was big then one would win by a bit most times. If the difference was small you may see either skeg or no skeg win at any time but perhaps one wins a bit more often.
The part of about a fixed course though is easy. You just pick some pier, point, home, etc. and measure with the GPS or map. It's nice to know the approximate distance but you don't need to know the distance at all. You care that one trial takes say 4% less time than the other.
Time should be measured carefully on some fixed distance and that's pretty easy to do. You could also use a fixed time and measure the distance but it's easier to accurately measure time.