couple things you need to realize.
1, in the beginning naruto was only using KCM. this was before he and kurama were friends. kurama would siphon out naruto's chakra to replace his own. so although he was using kurama's chakra, his was still getting depleted. then naruto used a bunch of clones which made that siphoning process increase even more.
2, naruto has been training and fighting for 2 days straight and still had enough strength to fight.
3, even after combining his chakra with kurama's, technically he is stillusing chakra.
4, he spread that chakra out among the alliance and controlled it . which drained a lot of his strength by the way.
after that he and sasuke both received chakra from the sage, so the point becomes moot by then. don't forget, naruto has ashura's chakra, which is the same as hashi's chakra. meaning naruto has a shit ton of chakra even without kurama's chakra.