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We have seen that Black Zetsu can keep a body alive that should be dead just like Madara was after losing to Hashirama. I think Kaguya was reduced to this black zetsu form after the fight with her sons. Not strong enough to do a whole lot herself physically. Madaras body was the perfect oppurtunity for her. She took control of his body from there on out. She knew how to make zetsu's and the black zetsu that "madara" created was just her transferring herself over into a white zetsu body. We know black zetsu can't make a full body of himself so once madaras body was used up Kaguya would need a new vessel to freely roam around in. Madara was in there basically being koto'd. Thinking it was his will but it never once ever since after VoTE