His Susanoo being stronger doesn't mean anything since Indra's Arrow would still rip right through Sasuke itself and vaporize him. Not to mention it doesn't explode, so he's 100% safe after the fact. Not to mention it's filled with the bijuu's chakra, so once Madara gets hit Sasuke uses Bijuu Susanoo to rip the Bijuu out of his body, and then Madara dies.
And no, Sasuke merged the chakras together inside his Susanoo. 9 Bijuu added together=the Juubi in terms of chakra. So they are both using the Juubi to get power. The only difference here is the Juubi IS the same as the Rikudo Chakra Madara has, or rather it's the source while Sasuke has half of Hagoromo's power and he has the Juubi's chakra. So there is no reason for Madara's Susanoo to be stronger.