Well the manga explicitly showed Kyubi in the fight against Shodai and Madara. So naturally kyubi knows about him.
As for the second kyubi attack on Konoha, Madara could be telling the truth that he was not involved. Only thing is that as the story stands, the kyubi is the only element connecting Madara to naruto's story.
If Madara is not involved in the kyubi attack and hence not in Naruto's storyline, then for all purpose Madara = filler ready to be destroyed by Sasuke primarily.
Any final villain should have Naruto as the main opponent. Sasuke, Sakura and others could be involved but only as a support team to keep the balance tipped in Naruto's favor. In other words, the final villain should have the strength to dominate the support team minus Naruto