Kind of explains where the eyes came from. The revelation that Madara possess the Rinnegan towards the end of his life and knows of Nagato as proved in a recent chapter may explain why he knows of Nagato. What i really do not understand is why give the eyes to a boy and what deal was made between Madara and Tobi. Perhaps its because Nagato was of the Uzamaki line thats why he recieved the eyes only to be manipulated in the future to bring Madara back to life..... Tho that never happened and the deal was broken perhaps by Tobi. Orchimaru knew of Nagato and he has something to do with this i feel.