its in Nagato's eyehole :|
He is a begginer of the rinnegan and i doubt he can use that as good as the Nagato and Madara i think he knew that and he didn't take chance's since it was war ..... and we still haven't seen him use the rinnegan
if I remember correctly he transported nagato's complete corpse into his dimension. don't know if he took out both eye's or just the one he needed for his eye. so the other eye is not accesable for others (except kakashi perhaps)
yes because he is not given up his own abilities, even though the rennegan is a powerful doujutsu, the ability to evade or 2 make someone miss because of his space/time dimensional movement