Here's a good primer on setup from ACI, no longer in business:
5) System setup
Getting the optimum performance from your sub(s) is going to require some careful listening. Keep in mind the sound you want. Using test instruments, test CDS, etc., can be helpful but also be fairly confusing. Low frequency room response testing is a complicated subject. Suffice it to say that inexpensive test equipment used without a lot of experience and understanding may give very misleading results. We suggest making your final judgment based on how music/film sounds to you.
Read your subwoofer owner's manual. It may give you all the information you need to optimize your system. The tips below may or may not be in your owner's manual.
-Placing the sub (s) near your main speakers is the easiest way to get a good match. The ideal placement is often somewhere between the main speakers. Placements outside of the main speakers can also work well. If you are crossing over below 80-100Hz, try a corner placement behind your main speakers. A corner placement is usually the optimum placement for maximum, undistorted output with the most accuracy.
-Instead of moving a heavy subwoofer around the room to find the best response try this simple trick. Place the sub where you normally sit to listen. While playing either test tones or music with a steady bass, walk around the room and listen for the deepest, tightest and smoothest bass response. Move the sub to the place where you heard the best bass.
-Placing the sub(s) close to a wall will increase bass output but may also make the bass less even. Moving the sub(s) into a corner will increase bass output even further. Use the placement to fine tune the bass your system produces.
-Placement of the sub(s) will often be determined by your room's configuration and furniture layout. Experienced audiophiles know that "fine-tuning" room placement can yield important gains in sound quality. Most listeners will be more than happy with the results they get from the most "convenient" placement. Very serious listeners will want to experiment with various placements to really optimize the match to the main speakers.
-Correct phase of the subwoofer is dependent on the frequency response of the main speakers, the crossover filters and the placement of the subwoofer relative to the main speakers. If you have a phase or polarity switch on your sub try both positions. The correct position yields the greatest amount of bass. If you have infinitely adjustable phase, dial it in until you have the greatest bass level. If you don't have adjustable phase, start with all speaker connections positive-to-positive and negative-to-negative. If there seems to be a gap in the response between the sub(s) and main speakers, try reversing the leads to either the subwoofer(s) or the main speakers. You will then probably have to re-adjust the crossover frequency and output level. The correct phase is the one with the most bass.
-Use (line-level) connections if you have line-outputs in your system. If you don't you will need to use the speaker-level inputs or adapters. The high input impedance of most powered sub(s) will not use any power from your receiver or amp.
-The low-frequency response of your main speakers must be considered. Crossover frequency should be set as low as possible. Lower crossovers will allow the subwoofer to audibly "disappear" and placement is less critical. The deeper your main speakers go, the easier it will be to get a seamless match. If your main speakers are a ported (vented) design, you will often get the best results with the vent plugged. A cloth or towel will work fine. Just stuff it so that you no longer get air pressure coming from the vent when the speaker is playing.