How do bass waves work?

I've just spent the last 3 days isolating my powered sub and main speakers. My entertainment room is an addition with a 4' high crawl space underneath the entire room. The sub was not only boomy but shook the room's contents. So, I placed the main speakers on 3/4" particle board which float on sand in DIY boxes. The sub is actually on a 2'X 2' X 4" concrete garden tile which then rests on the sand box. These sand boxes have spikes to the floor. It worked - hardly any speaker energy is being transfered to the floor. The bass is incredibly tight and the highs are crystal clear. I have EQ'd my LF cross-over with the help from a concert violinist. Yet,when I play music with heavy bass (such as cut #1 from the Titanic soundtrack) my room still vibrates - but the not the floor that the speakers are sitting on. Why might that be? Thanks!
The speaker cone vibrates causing sound waves to travel through the air by alternately compressing and decompressing the air. The sound waves make your eardrums vibrate. Thats how you hear.

These same sound waves also cause other things in the room to vibrate. One of the goals in a well designed listening room is to minimize these secondary vibrations as they add to and color the sound.
I am not an engineer or physicist but may be able to comment on your bass problem. First, when you say that the room vibrates, do you know what part of the room? Any part of your room may become excited by bass energy, including your floor in a area more distant from your woofer.
In general, all rooms have one or more resonant frequencies based largely on their dimensions, internal volume, and materials within. Deep bass notes have extremely long wavelengths and are essentially more omnidirectional as the frequency decreases. They will not behave in a focused manner as you will experience with higher frequencies. Bass energy also tends to build in corners in the form of standing waves. If you play a test disc with specific low frequency information and use a Radio Shack DB meter, you can walk around your room and see the peaks and nodes as measured on the meter. Note that these meters have their own inaccuracies in lower frequencies but will be adequate to give you a general understanding of how your room is behaving. A number of test discs are available with steady state frequencies. This would be the cheapest way to get a relative measurement of bass energy in each location at different frequencies. You may also want to listen for vibrating items within the room. Moving the woofer within the room will effect the energy in specific locations dramatically. Additionally, there are many links on Audiogon about this problem and recommendations including bass absorption devices so I will keep my comments brief and general. Make sure you read links about speaker/woofer placement as this is critical.

Hope this gives you some guidance.