<font color='#008080'>This doesn't make any sense... You connected a rear center channel line out of the receiver to the sub line in, instead of the sub line out of the receiver?
The reason this makes no sense is that I would have thought that you would have configured the Yamaha not to even have a rear center - thus NO sound would be coming out of that line output. The only bass you shoudl have heard at that point would have been your mains.
Here's what you need to do:
1. Set up your receiver for the speakers you actually have connected (i.e. NO rear center, no effects speakers, etc...)
2. Set the receiver up for speaker sizes (i.e. unless your mains are larger and go down to <40 Hz, set them to small, along with all other speakers)
3. Set your sub output to SUBWOOFER (or BOTH if your mains are larger and handle <40Hz)
4. Play with the sub to position it correctly. Follow the directions in
this article
Listen again and report back here. Enjoy! As a side note, Steps 2 & 3 settings can be played with. As I don't know your system, you may find that different settings work better for you. In general, LARGE means it can handle low (I'll say <50Hz) frequencies with grace and ease (not just the specs on the box). If you have ANY kind of bookshelf speakers as mains, I'd set them to small, along with the center and surrounds.</font>