Ric, welcome to the world of subwoofers.
If you notice the woofer booming on certain albums the level is too high. turn it down just a little at a time. There are two parts to this, the sound and the impact. I use two types of music to evaluate subwoofers. A solo acoustic bass (Dave Holland Not for Nothing) and a drum solo (Grateful Dead Infrared Roses.) I use the bass to adjust levels and the drum solo to adjust phase. To start get a tape measure. You want to place your speakers on a radius from the listening position. The two subs should be between the satellites right up against the wall. With front firing woofers I will turn them facing each other so that the side of the driver is right up against the wall. The satellites are just lateral to the subs at the same distance from the listening position again on the arc of a circle. This is a good starting place. Check your levels again. This may take several days of listening to get right. Then play your drum solo and listen (or feel) to the impact of the bass drum. Move the satellites back and forth, towards and away from the listening position until you get the most impact.
If you are not using a two way crossover (running your satellites full range) keep your crossover low like 60 Hz. Unfortunately this eliminates 1/2 the benefit of using subwoofers. To get the most out of them you need a dedicated two way electronic crossover between your preamp, amplifier and subwoofers. JL Audio makes one. This roll of the satellites, lowers distortion and increases the system's head room (goes louder!) In this case you can take your cross over up higher like 100 -125 Hz.
Ultimately you would have digital bass management like the Anthem and Trinnov units use. Then you can put the speakers anywhere you want and the system will correct it.
Always evaluate the sound from your listening position. Bass can change quite dramatically as you move about the room. If you think something sounds off go check it out at the listening position. It may sound fine there.
Done right the subwoofers should disappear. All your speakers should disappear leaving just music. Doing this analog is not easy. Over the years I have lost plenty of hair on this issue. It took me 30 years to get it just right.
As a note, multi subwoofer systems like the Audiokinesis Swarm make setting up a subwoofer system in the analog world much easier as they take phase out of the subject so you only have to worry about levels and crossover points. Phase and time are easily the hardest to get right.
