I would suggest that you pull down some of Harman's white papers on this subject. Their research found that using two subs helps to make the bass more even overall. (the placement in their diagram had one sub along the middle front wall and another one along the middle back wall, obviously you would need considerable space behind your listening position to accommodate this setup) With one sub, you're more susceptible to room interactions that create huge peaks and/or nulls. These can be remedied with careful placement, room treatments, and parametric equalization. But, using two subs is another (and some would argue more effective) way to help alleviate some of these room induced issues.

As kex pointed out, the auto calibration function on that Yamaha receiver does not correct far enough into the bass frequencies to be effective for subwoofer integration. You might need to get an outboard parametric EQ to address any room-related problems that might crop up in the 20-60 Hz range (this is the majority of the audible range that a subwoofer is supposed to cover).

http://www.harman.com/wp/index.jsp?articleId=1003

With regard to a 7.1 speaker setup, keep in mind that if your sofa is right up against the backwall, you're probably better off sticking with a 5.1 setup. The positioning that Dolby recommends with a 5.1 setup is to raise the surrounds about 2' above ear level and point them direclty at one another in order to diffuse the sound sufficiently while retaining some degree. I also like placing the surrounds about 110 degrees off center (this is only slightly behind the listening position).