Just so I know I'm reading you right, when you say "9.2.1" are you saying 2 subwoofers and 1 surround channel? That's what HD meant when he said the sub(s) go in the middle. If you have 1 sub and 2 back channels it would be 9.1.2.
Like he also said, with that many speakers going it's not a horrible idea to get a separate 2 or 3 channel amp to power your main speakers or mains and center channel to take a little of the load off your SR6013, but that would be a "down the road" type of consideration, IMO.
It sounds like you have a capable HT setup and enough speakers (for now, lol) with the 6013 so the focus is on your "if you hear music don't come knockin'" room? And for that you so far have the Onkyo, Klipsch sub, RP160s and still need a player? For now, the Onkyo should serve pretty well as the hub and powering your speakers in stereo, unless it's lacking any features you need. I think for the sake of not getting confused we should deal with your 2 setups separately, if I'm understanding you correctly (I have comprehension issues sometimes so please correct anything I said that's incorrect). I think I'm getting a little lost between the 2 setups being discussed.