Naruto has his own large chakra pool. kakashi has said it at the begining of the manga/anime. He said "Naruto has more chakra then sasuke, even more chkra then me" or something along those lines. Neji has also said he has a large amount of chakra. Remember the training with jiraya, he told naruto to waste all his chakra and it took forever, and the point of that training was to only have the kyubbi chakra left. All those points prove naruto has his own extremly high amount of chakra. The kyubbi chakra is more of a second chakra with a penalty behind it of going berserk.