Hey, fantastic news that your speakers are working like you want!
Now, for the sub. I'm assuming that you have it connected using the subwoofer output jack (RCA style) on the receiver. If not, please let me know.
Here's what I suggest we start with (some of which you may have already done):
1. Using page 24 of the owners manual as your guide, set the front speakers to "Small" and set the subwoofer to "Yes".
2. Using page 25 as your guide, set the cross-over frequency to 80Hz (just as a starting point...you can adjust to taste later).
3. On your sub, either set it to bypass the cross-over (if available) or adjust the cross-over to the highest possible setting. The reason for this is that the receiver will be deciding which frequencies to send to the sub, so you want to disable any filtering on the sub itself.
4. Again using page 25, and actually before the cross-over section of the page, adjust the channel levels manually. If you have an SPL meter...that would be great. The goal is to have the volume level from the left speaker, right speaker, and subwoofer be the same. If you don't have an SPL meter, try to make them sound the same to you. If you have trouble getting the subwoofer to sound loud enough, you can go between adjusting the volume level on the sub itself and the channel level setting for the sub on the receiver.
Check that out, and please let us know how that works. Thanks.
Adam