What does one do to deal with bass that is significantly a little too much (and sometimes much more than a little too much) while the rest of the range is at a quiet or normal volume?
Welcome to the wonderful world of room modes.
First of all, you did adjust subwoofer volume when setting things up, right? Needs a bunch of sine test tones, from about 150 Hz down to 20 Hz or so (most easily generated on the computer with Audacity or whatever; the CD that I have starts at 10 Hz intervals, then goes to 5 Hz under 100 Hz, and 3 Hz under 40 Hz). A logarithmic sweep of that range tends to be quite useful, too. They say a pro will adjust for 10 dB too much and a layman for 20 dB, so make sure to do a check with music in both plain 2.0 and 2.1 or whatever.
The test tones will probably reveal a rollercoaster ride in terms of frequency response, but that's pretty much normal for an untreated room. An old trick then is to place the subwoofer in the listening spot (including height) and walk around in the room, looking for a spot that minimizes resonances (sweep is useful here). Then place the subwoofer right there. Reciprocity FTW.
At this point there may still be some unevenness in the crossover frequency range (which should be set up as low as the fronts will reasonably allow). The subwoofer's phase control may take care of that. Theory says things will go funny if main-sub distance exceeds half a wavelength, which is hardly 1.2 m / 4' at 150 Hz, so keep that in mind as well (that's not to say that you couldn't get a good result otherwise but consistency across the room is likely to vary).
As a rule of thumb, room mode excitation is maximum near the borders (walls) and minimum in the center. Unfortunately many subwoofers need a bit of help from nearby walls which happen to increase levels as well. Sub construction also figures in here - a downfire sub is to be considered an effects device as it deliberately gets the speaker as close to the next surface (floor) as possible.
If you've got some really nasty resonances, some Helmholtz absorbers tuned to the offending frequencies may bring relief.
It is always a good idea to make sure that the floor isn't excited by the sub. Some types resonate very well and may require some concrete blocks or similar (box filled with sand, whatever) under anything emitting bass.
The pros will tell you that a single subwoofer in a room is an exercise in futility anyway. Ideally you'd have a double-bass array (DBA), or at least a single-bass array (SBA), such that the bass is emitted at the front and "sucked in" at the back without being able to build up resonance. Now only a few of us will want to pay for a bunch of subwoofers, but even two of them can already be used to improve frequency response and consistency across the room.
