The neck extension is usually used if you are adding a considerable load to the tank or if you are adding additional tanks or upgrading your system but do not want to purchase a new skimmer. If your skimmer was working correctly before and you added the neck extension, it may not work as the skimmer/tank is already at a good balance and there may not be enough organics to compensate for the new 3" of height. Lowering up the skimmer will raise the water level inside the skimmer chamber and therefore nullifying the 3" of space you added at the top.