It's best to blend the sub with the mains. Set the sub crossover, near the natural roll off point of the stereo speakers. Don't over-lap the frequencies too much, as that can cause bass boom. Play some test tones to help with this, especially sweep tones. Tons on the web that can be streamed. Then, don't set the sub level too loud. Slowly adjust it's volume knob, to where the sub is just heard at the listening position. Not too loud, to where you want to scare the neighbors. A subtle level is key. Once you reach that point, play some well recorded acoustic music. Dial the sub in more if needed. Then when you're happy with the sub's performance, turn it off mid song. Did you hear the sound collapse? Loose ambiance? That's good, as that's how it should be. Again, the sub should be a subtle addition, that shouldn't draw attention.
Also, experiment with sub placement first. If set at a good crossover point, it doesn't have to be next to the mains. It should blend well if set up properly. Use the old tried-and-true trick of setting the sub at the listening position. Then walk around the room as the music plays. Is there on spot in the room, where you like the subs performance best? If so, put the sub there. It should then sound the same in the listening chair. Now it's time to tweak the crossover point and levels, as I mentioned above.
Good luck!
