Im sorry to even make this thread, since the idea of chakra is made up in Naruto world, hence it is subject to contradictions. However, i can pretend that i really care about how chakra works.
@Oldmagic: thinks that ppl in Naruto are born with blankslate, no chakra to start with.
So Naruto's current state must come from his genes or experience. Chakra growth could be due to both genes and experience (this include having the Kyuubi inside). So the end result is that as Naruto grows, his reserve of chakra increases the following possible ways:
1. independently of the Kyuubi
2. OR Kyuubi's chakra is being converted
3. or both.
Option 2 seems unlikely, because a normal person is capable of having chakra, big or small...so Naruto must have chakra that is his own (not converted from Kyuubi)
If option 1, then Naruto chakra's growth rate is better than normal...but Oldmagic is right that it doesnt require Naruto's chakra to hold the Kyuubi when the seal first applied...But this doesnt rule out the fact that the seal require chakra to operate, so when it was first applied the Fourth put his chakra into it, then later Naruto chakra's takes over the job. The plain fact is that its pointless to battle the Kyuubi with chakra, it has unlimited charka! So if the seal is wearing off and Naruto need to apply his chakra to hold the Kyuubi then he wouldnt be able to use his charka to battle at all.
If option 3, Naruto own's chakra is small, but the total is large, since part of the Kyuubi's unlimited chakra is converted for Naruto. Its never the case that Naruto become tolerable with himself, that dont even make sense, but if u mean the Fox and naruto is practically one, then we are saying the same thing in different ways (so dont flame me) because this is the Theory i am supporting. The Kyuubi is supplying Naruto with its chakra, so that naruto is becoming stronger, and is also able to tolerate the damaging effect of the Kyuui's power. Of course this theory doesnt support the idea that chakra is need to hold the Kyuubi...rather the Kyuubi is sealed by the Fourth and is stuck with Naruto, untill further notice. For me this makes more sense, with the fact that Naruto can use his chakra until empty, then he use the Fox's.
Jiraiya's conjecture that naruto should harness the Fox's power, hinting the dependency. yet Kakashi says: Naruto should use his own. At first gloss, they are opposite, but to me they are the same, just being told from different level of abstraction. Kakashi made naruto more confident in himself, while Jiraiya is better at understanding Naruto's power. Its not the first time we see Kakashi tells his students white lies to guide them in the rigth direction. Thats what make him effective teacher.
Now, Yamato had to suppress the Kyuubi during training mainly because that help naruto focus on developing the jutsu, since the Kyuubi only cooporate with Naruto on some level, the more tails appear, the more the Kyuubi takes over. But eventually, Naruto will handle the Fox better and gets too use more of the Fox's chakra/abilites...But in the end, the Fox is very much indepenent of naruto in term of strength, such that if someone reverse the seal, the Fox can be free again...like Gaara and OneTail...Gaara gained strength from OneTail, but after it left, Gaara is still capable (many speculated that). and now OneTail has his independent (of Gaara) existence elsewhere.
I think at this point, the confusion is cleared, at least for me. but if anyone still want to participate, go on ahead, but make sure you cover all ground in ur arguement if different than mine, so to be more convincing.