I like what many are suggesting and hinting at here. Yes, you are dealing with a game of "find that frequency response" here!
I would start by playing some test tones(bass) through your sytem, and measure with a Sound Level meter (yes, EVERY audio-enthusiest needs a Radio Shack SPL - NEEEEEEDS!). This will tell you "which" frequency-response holes you have in your system. Then, you need to find out where they are, and place either, and/or both the speakers and your seat where those AREN'T!
Your goal is flat('ish) frequency response from the speakers and sub from the listening position(s), as a foundation, yes. Without some semblence of "balance" here, you'll never have an accurate, dynamic, well balanced, hi-fidelity fundamental sound from your system - and you'll be up and down on the volume, with wither holes or nasty irritating peaks to the sound, indeed.
In your case, without reading too much of what you wrote, sounds like either your sub and/or your speakers, in relation to your seat(s) are sitting in a null, or nulls.
I might recommend both placing the sub where your ears will be seated, and moving around the room in places where you are considering locating the sub, to find the most solid, even, non-boomy, fast, musical, dynamic spot for the sub (playiing some solid bass material, and some test discs to measure, sure). Also, do the same for the speakers - making sure you have solid bass where the speakers and sub cross, too.
You can start with the sub/speakers in a corner, and then play some frequency response test discs - available in lots of spots around the web - and then move/listen/measure around the room where you can place your seat(s), to find a good response location, and where all the nulls are (as to avoid).
yes, it's a process - even more so without meters and instrumentation, for an expedited process. Otherwise, take your time. The results are WELL worth it...