Fine-tuning the sub: Takes time & dedication.
If your sub can get to 25hz or so, try to balance it with your front mains.
But like I already said, for music 2-channel stereo only, it is a little more touchy to properly balance, but you can certainly come up with the best compromise. It's surely worth trying in your case.
And for movies, again, it is much less important, as you probably already know.
Good luck,
Bob
* Note: My best advice is that you take your time, use a Radio Shack analog level meter, and even try different subwoofer positions. Be patient (it might take few days to get the right balance where you are satisfy). It's all about experimenting, fine tuning and patience.
Also, on your subwoofer, try different position(s) from the Phase switch of knob. You want tight and loud bass, for the best Phase position.
But positioning your subwoofer at the right place is the most important aspect for best integration with your two front main loudspeakers.
And don't forget to set the Low Pass Filter on the back of your Sub at the "Bypass" position, or to it's Maximum position if the "Bypass" is not available. Plus set the X-over from your Yamaha receiver at somewhere around 60hz or so (you'll have to experiment with various x-over choices).
Also, if your sub has a High Pass Filter, set it to it's lowest position.
Furthermore, set the gain (volume level knob) on the back of your subwoofer at about 1/3 of it's rotary knob position. And adjust the final volume level from the subwoofer channel level of your Yamaha receiver (use your Radio Shack level meter to help you out).
** Tip: Put the subwoofer at your listening position, put a CD with good bass content, and crawl on your knees around the room for the best low integration possible. What you're looking for is tight bass, with good clarity, punch and resolution. The Radio Shack level meter will help you to get in the right ball park. You also need a test disc with the proper test signals, like Avia audio & video test DVD from Ovation software, or Video Essentials DVD or Blu-Ray audio/video test disc.
*** As you can see, it is a delicate balancing act.
--> Check here at Audioholics on some articles for Subwoofer positioning and Integration with the Main loudspeakers. And also visit the web site of "Secrets of Home Theater and high Fidelity" for more excellent articles on this subject.
**** I'm still fine tuning my subs after over 20 years.

But then, I am a very patient man.
