Bro Lawin,
Here's an advise I've read from the net: To find the best position for your sub, EXPERIMENT! and literally get on your knees and hands and start crawling! To discuss room acoustics would require us a whole lot of time and space. There is generally no specific rule when it comes to speaker positioning since each room has its own individual acoustic characteristics. Each room is unique. So, it would probably take a an expert to set your system up to it's optimum performance configuration. But who can afford a professional? Especially us who are on a budget. So, I guess you already found the secret, experiment! And please, never underestimate your own ears. What good is a setting that's been done by experts and professionals if it doesn't sound good to you? And to think it's YOUR home theater. It's quite hard to do a diagnosis on your equipment unless you have a totally neutral room. If you can afford to have your entire HT room acoustically insulated, then maybe that's the only time you can actually say what really works for a certain kind of equipment. Besides, as they say, experience is the best teacher, so let your ears learn more everytime by constanly listening to different systems and sources, and maybe you'd also find what suits your taste. What I can do is help you with some useful infos. Give me your email ad, then I'll send you some materials I found to be helpful and might aid in answering the questions you have.
Just a question, bro, is that 2 inches and 8 inches? Or feet? And I really wouldn't wonder why you have a lot of vibrations in your room. Why? Well, for starters, if you have the Euros 8 towers, definitely! Those babes have dual 8-inch drivers and can go down to 50 Hz, why wonder? And remember, subs and speakers that can generate great LFE signals should be given room to breathe since they move around a lot of air. I'm quite sure your towers and sub are both often generating the same frequencies, that's why there seems to be an "over-adequacy" of bass in your room. That's why when you set the other speakers to SMALL, you experienced cleaner and better bass reproduction since that setting filters out all the frequencies below the set crossover, say 90 Hz, from all the other speakers to just the sub. Kaya siguro ganun ang effect sa room mo. But that's just a theory.
Oh and aah, you may be hearing better bass sounds in your dining probably because, your HT room already filtered out all the room reverberations and mid bass frequencies and other impurites and left out all the lower bass frequencies for you to hear, since the lowest bass signals are the hardest to contain, that's why you hear this cleaner sounding bass.