My preferred method for subwoofer hookup (and best integration) is to run the sub parallel to the main speakers off the speaker outputs of the amp, or from the speaker inputs themselves to the high level inputs of the sub, as opposed to from a preamp output to the low level inputs. Allow the main speakers to run full range (avoiding running the subs high pass filters through your main speakers), and only use the sub to augment what the mains do.
The theme here is to feature the speakers, not the sub. Set the low pass frequency of the sub at a very low setting (40-50hz if possible), then set the gain very low so that you only hear the sub in very bass heavy passages. You'll need to experiment with sub placement and the phase setting. If done well, you'll barely hear the sub, except on passages where there's a lot of bass content, and even then it should be more felt at the lowest frequencies than heard. YMMV, but this is what's worked best for me.