Personally, I would set the system to a 2.1 configuration for music and 5.1 for HT. This means integrating your sub to your mains for both. It will take some careful work and patience to get it set correctly, but the benefits and the sound is well worth it. On my system, I have configured for music first and foremost.
Set all speakers on your AVR to "Small" and make sure the distance from all your speakers to your listening position is set correctly on your AVR. Now, a lot of owners of floor standing speakers have an issue doing this because they believe that it is a waste to set floorstanding speakers to small and not us them as full range speakers. Keep in mind that a crossover is not a brick wall. It simply reduces the sound level of frequencies below the crossover region logarithmically. But the change is very gradual. So while you may set your crossover to, lets say 80hz on your AVR, the actual content of frequencies below 80 hz that are still going to your mains is very significant, (I believe only reduced by 12 dbl @ around 40hz depending on the crossover order, and even less for frequencies between 40hz and 80hz). In any case, even set to "Small", you are going to have a very significant amount of low frequency content below the crossover point going to your mains. What this does, however, is to transfer the lower portion of the frequencies to your sub... the driver designed and built to handle these frequencies, (and do so far better than your mains can). Because your sub is self powered, it can handle these frequencies far more efficiently too. Driving a full range speaker is a huge power load for most commercial AVRs. And the biggest power load is in trying to generate those lower frequencies at a level and dynamic range equal to your mids and highs. It take a LOT of power to do so. When you free your AVR from having to cope with the power requirements of those low frequencies, the receiver is then able to dedicate that power cleanly to generating the mids and highs. You get more uniform power and a greater overhead for your mains. The sound improvements and dynamics from your mains will be very significant. From a cost effectiveness standpoint, a far better solution, IMO, than biamping or biwiring. Your low frequencies will also sound better becaue you will have a self powered low frequency dedicated driver that will be able to keep up with the rest of the system in terms of power, tonal accuracy, and dynamics.
Now, keep in mind that the goal is to set your entire system to as flat a frequency response as possible. Remember the room where the speakers will be in will be a large contributor as to how your sound system performs. If the room has acoustical issues, (lots of reflective surfaces, dead spots, etc), it won't matter how good your sound system is. So identifying and treating the room properly is paramount. Second, don't rely exclusively on your ears for your initial calibration. Your ears can and will deceive you. You have spent a lot of money for your sound system. Go a little further and invest a little money on a calibration DVD such as AVIA and a good SPL meter to calibrate your system properly, and make sure your SPL meter has the proper adjustments incorporated before your calibrate your sound system. When you calibrate the sub, you will initially notice, (specially for music), that the sub seem to be somewhat subdued at first. A good quality sub is supposed to complement your speakers... not overwhelm them. The sub is supposed to convey the low frequency content if and only when the content is there. In fact, a well integrated sub will virtually dissapear and the content will seem to be coming from your mains instead. Some folks like to have that little mid bass ump, and they run the sub a little hot to provide this. I personally like the sub to simply complement the mains for music. Once you have initially calibrated your sound system with a DVD calibration disk and an SPL meter, it will only be a matter of making very minor adjustments for your own personal tastes. I have found, (and this is only my opinion), that once you calibrate properly for music, HT applications will take care of themselve. Your bass should be more noticeable if you set all your speakers for "small" and you calibrate with AVIA, for example, because AVIA takes in consideration the sum of all low frequency content in a 5.1 configuration that is being redirected from all speakers into the LFE channel and will calibrate correctly for it's content. The end result is great bass with non of the bloat.
Good luck and enjoy your new system!
Sony KDP-51WS550 HDTV, Yamaha HTR-5660 Natural Sound Receiver, Yamaha CDC 555 Natural Sound CD Player, Mitsubishi DD-6040 DVD Player.
Klipsch RF-82 Mains, RC-62 Center, RB-61 Back, SVS PB12-NSD Sub... Promedia 4.2 THX in the office. Grado SR-80 Cans.
Welcome... to the house of Rock!!!