Two schools of thought.
First, I am not sure the length of overhang makes much difference. The skirts tend to get blown out by the internal air pressure. Many a chart has been lost in flight by being sucked out the gap. For the RV6, unless you modified the fuselage, the front part of the skirt was cut flush with the top rail for about 6" to allow it to clear the side skin due to the shape of that part of the fuselage. You then transitioned to more overhang.
The second thought; if your unhappy with it, it does not take long to make new side skirts the way you want them. To go back later and change them would be a royal pain....