If you purchased a new surround sound system recently, you may have experienced some difficulty balancing the sound, especially your sub-woofer. Most systems today automatically set the speakers to the desired level, but not the sub-woofer. Remember, theses settings are often default settings, or are geared to someone else's preferences, not yours. I use Klipsch speakers for surround with a Yamaha sub-woofer, because I could not find the sweet spot on the Klipsch sub-woofer. For some strange reason, subs are not included in the auto setup, manufacturers leave it up to you. I substituted the Klipsch with my old Yahama sub, and the sound and balance is perfect. Here's the fastest way to set your sub-woofer.

Start with the crossover. Slowly turn it up until it fills out the gap in the sound. In other words, your speakers are set to your liking, but it still sounds empty. The sub fills in that emptiness. You want your system to sound full. As soon as you achieve the fullness, stop and leave the crossover right there.
Next, adjust the gain. Select a channel, (I always use ESPN), then turn the sub-woofer down until it's silent. Now, slowly turn up the gain until you hear the bass start to fill up the emptiness, and it starts to sound full.  Stop right there, that's where you should be.

You may also have a phase switch. If so, switch it and see if you hear a difference. One may sound better than the other depending on your room size and system. On my system for example, the sound remains the same, I notice absolutely no difference.

That's all there is to it, you're all set up. Now get ready for some sweet sounds for your new system!