Hey Jarrett,
I have the 1804 too, but don't yet have the sub.
A couple of observations on setup, though. You might look around here for "calibration" threads, or those including the phrase "SPL meter" (I'm too lazy to do the search for you right now - sorry). I bought the Sound and Vision setup DVD and am happy; others have Avia or Digital Video Essentials and seem pleased, too.
Now, buying a SPL meter and setup disk is a good way to go, but I can understand you being reluctant to spend the ~$70 if you have neither of those things already.
HOWEVER, you should still go through the on-screen Denon setup stuff. When you go through it the first time, I would use the sub volume to do the setup and leave the 1804 sub output at 0db. Doing it that way will allow you to use the Denon sub adjustments (by 1 db up or down) to tweak as you listen in the future without having to muck around with the sub volume.
Also, be sure you have the sub crossover all the way "out"; since you are running the sub from the "LFE Out" of the Denon rather than through the speaker-level outputs (right?), you don't need to utilize the sub crossover.
What kind of material is causing you to perceive boominess? I am not among those that subscribe to "break in" of the equipment, but I do think that your perception of the bass will undoubtedly change over the short term.
Likewise, the suggestions to move the sub around, even by inches, could help tame standing waves within your room.
