I've managed to improve the bass a bit in my truck (Laramie, 8.4" 4C Nav, HK stereo).
First I packed some shipping blankets behind the rear passenger seat over the sub which helped mute it a bit, but not enough.
The bass has a strong boost in the mid-bass frequency range (maybe 60Hz - not sure don't have a scope) that overwhelms the rest of the bass response making it very boomy without clarity, and the EQ seems to have no affect. This is with the mid/treble at their nominal setting (0) Basically all you seem to hear is the dash speakers and the boomy sub with very little from the door speakers providing midrange.
Sound output is driven through a DSP and the EQ does not behave like a traditional analog EQ. I've done a lot of experimenting with the EQ settings to see if there's any way to manipulate the DSP to reduce overall bass levels, and I found that by boosting mids to +5 and treble to +3 it seems to reduce the bass gain and bring the door speakers into play. It also makes the bass EQ more effective such that I now have it at -3 rather than -8.
Sounds much better, but still not as good as it should. Next I'm going to try adding some polyfill to the subwoofer box which hopefully mellow it even further.