Madara can use Susanoo while his Rinnegan is activated. I think it was shown at the end of 561, when he's dropping the meteor. At that point, he still has Rinn activated but also has Susanoo activated.
The bottom line is that if someone awakens Rinnegan naturally, he/she can utilize all the levels of techs he/she has unlocked to that point with Rinnegan. For madara, this not only includes all natural rinnegan techniques, but all Sharingan techniques as well.
As for Nagato, its assumed that since his Rinnegan was transplanted (as most people think) he only has access to natural rinnegan abilities and has no inherent sharingan abilities built into them. If the whole transplant theory is correct, than a transplanted eye cannot change from the form it was transplanted in. That would mean that since he can't switch back to sharingan, he also can't use those techniques with his Rinnegan activated.