We can probably get into audio geek territory pretty quickly. I guess it depends on the system you have put together. My opinion is that the system you describe is one where the sub is used to extend the bass of small bookshelf speakers. The main speakers are designed to drop off around 100 Hz or so, and the sub is used to fill in the bass below that. The thoery is that bass is non-directional to the human ear and you can't locate the source. Unfortunately for me, I am able to localize bass down to 60-80Hz, so I hear this sort of sub kick in and immediately notice where it is coming from. It is annoying to me to hear a motor start up on the left speaker and hear the lower frequency component comin right of center.
I'm not trying to knock satellite/sub systems in particular. They work in a lot of situations. I have one myself in my family room. We don't do critical viewing or listening up there, and keeping the speakers small was a consideration. However, down in the theater, I find I much prefer full range main speakers. I run Klipsch KG-4s down there with a 10" woofer and clean bass down to about 50 Hz. ON that system, I fill in the sub duties with a Velodyne RF-12a, which has its own 1200 W amp. I set the cutoff at the receiver and sub lower, to mostly give a boost below 50 Hz. The effect on my system is smooth bass at frequencies you generally hear coming from the main speakers, and sounds you feel coming from the sub. When the sub kicks in, it mostly shows up as a pressure in your chest.
I was trying to differentiate between the two types of system philosophy in my earlier post, but didn't do a very good job. My understanding is that Jason/Elway has a system closer to mine, as he upgraded main speakers a few months ago, so my comments were directed that way. Jason, I am not a big fan of dual subs, unless you are very careful on placement and matching. It doesn't seem to make much difference in smaller rooms. In larger rooms, it can improve sound by lowering the reflection time from the far wall. Most people who do it recommend placing the subs in the middle of the front and back walls, and place them some distance from the wall. If you look at this picture of my HT setup, you can see that my sub is about 18" off the screen wall. The room is only 13x20' and I don't feel it will help much to add the second sub though.