Its not going to hurt anything using the larger tube's. In theory it sounds correct but honestly there has to be an advantage using the 6' tubing. Not a ton, but i'd say some advantage. The biggest prob is all the backpressure on the pump at that height. Not alot of pump's do well with that much height. OR's, eheim's and large laguna's are going to be your best bet. There's so many pro's and con's when it comes to a 6' vs 3'. If you start from scratch your better off with the 3' due to cost and efficiency. Its much easier to inject air into a 3' skimmer than a 6' and its going to take less wattage to pull the air due to less backpressure on the pump. Its also easier to hide a smaller skimmer : ) The pro's of the 6' are mainly great dwell time. The cons are harder to inject air, eye sore to some and its going to take higher wattage to get the right amount of air.