What room correction does your PC use? And how sophisticated is its bass management? The NR709 has MultiEQ XT and it's hard to imagine your sound card will produce better quality audio than your receiver. MCH analog also bypasses features such as Dynamic EQ and Dynamic Volume. Once you get all six channels working, you'll need to do a separate manual calibration since the receiver's auto setup only affects digital processing.
As for only getting stereo, have you set the Audio Selector priority to MultiCh? (p55 of the manual). This should be pretty straightforward. Plug in the six cables. Select BD/DVD and MultiCh on the Audio Selector. At that point, your AVR just does amplification for the analog inputs. There's no other processing involved.