You need to remember that Naruto wasn't directly controlling the chakra of the Kyuubi, otherwise Sasuke's Sharingan could have percieved his motions.
It is likely that Naruto knew what he wanted to do, and the Kyuubi just did it, he IS a Younma, after all, you don't become a superpowerful demon-god without enourmous Chakra and perfect chakra control - I suppose that would also explain why Naruto managed to do the Rasengan with one hand, the Kyuubi would have helped him.
This is all speculation, however - I just like making sense of what I see, rather than just saying "The anime is stupid and the writers have no idea waht they are doing."