I guess I have always run a 5 channel system, not 5.1 channel. I never liked how the sub integrated with the movie soundtrack, and came to the conclusion after trial and error, that it was not the sub (REL Q100E). Adjusting room accoustics was not an option.
The REL also has high-pass connections that run the sub off the signal from the speaker terminals. This is usually how you run the sub for 2 channel audio. I set the HT receiver to "no subwoofer" which sends the entire signal to the speakers so they run full range. I then set the sub in high-pass mode below the speakers so they just fill in the bottom the same as for 2 channel. In our family room this works much better. The bass was too localized for my taste when the sub did most of the work in 5.1 mode running through the subwoofer pre-out.