Time travel is incredibly complicated as a concept. But, given your premise, we can eliminate the quantum mechanics, I think.
So, there will be a jutsu that will send Naruto back in time, presumably to a time where he also exists. Will the jutsu supersede his consciousness, or will his two selves co-exist? I'd posit that having the future version of Naruto act as sort of a mental voice of reason might be better, and more believable.
Then there's the paradox theory, that simply by altering the flow of the future, you change more than you anticipated. The whole things works on the principal of the butterfly's wings: a butterfly's wings flapping can alter air currents, and the change ripples along until you see an upheaval in the weather patterns on the other side of the world. So, Naruto will need to be very careful in how he alters events, or at least should have that concern in the back of his mind. He can't be rash and brash.