More panels allows 2 things - strategic placement of the seams as well as a more exact fit. The more panels can mean the shorts don't move around on you as much on the ride or that the shorts stretch in the right places (no binding). You'll find that more panels cost more but you'll also find nicer items like better chamois and flat-stitched seams (do I have the right terminology, Irulan?). All this means comfort and no chafing, or at least less chafing.

SK