It can make a great deal of difference. With a skeg located at the far stern of the hull it will greatly reduce weathercocking, greatly strengthen the tracking but it can also cause the kayak to yaw more from rear quartering waves. With the skeg located more foreward, toward the cockpit area, it will still reduce weathercocking without effecting the maneuverability as much and also reduce the amount of yaw from rear quartering waves. This more forward location lets it work as a a fulcrum also. If your installing a permanent skeg it's best to tape a temporary skeg in different locations along the keeline to find the sweat spot for that particular kayak and paddling characteristics your looking for. I locate my permanent skegs as far forward as I can until the weathercoking is reduced to a manageable level. This allows the kayak to still have most of it's maneuverability and the greatest reduction in yawing from rear quartering waves.