The length of the skirt is measured from the bottom of the spa cover to the end of the skirt. Typically the skirt should be long enough to cover any of the exposed spa shell*. If your spa is of a top-rail design be sure the skirt isn't too long so it pushes the cover upwards. If you're covering the entire top-rail, you may want the skirt long enough to also cover the side of the rail.
* Given no obstruction (left side of picture above) we would recommend a slightly longer skirt.