I've got the Ultra13 and it'll pound me in my main seating position, but stand up and it goes away until I take a step forward. AND I've got TWO Ultras to boot! So, placement can be the biggest culprit. Next, I'd get an analog needle radioshack meter or good mic and run REW (a program) sweeps thru the system to see what's going on and if there's any nulls. Audyssey will cut peaks a lot but can't do much for valleys in the frequency response.
With your Marantz try running the subwoofer XO at 120Hz since that's the spec. the LFE channel is supposed to cover. Then set your mains to small and play with that XO until it blends seemlessly. This will take the mains audio (movies and all stereo content) and parse it out between the mains and sub. If your mains are well placed for good imaging and mid response they'll likely be in a compromised location for good bass. I have my B&W towers XO at 60 right now. Occasionally I try 40 and have been all the way up to 80. For fun try the mains XO set to 100 or 120, 150 etc., to see how the Ultra plays that upper region of bass versus your mains. With the sub out XO at 120Hz, movie bass content over ~80Hz on the LFE channel won't be cut.
Ultimately, the Ultra is very capable across the entire sub15 - 150 Hz range, but these lower frequencies are also VERY dependent on room and placement. There is the odd chance that the sub's forced placement, orientation, etc. due to its size, might not work well for you and your room. I partially have this problem in my living room setting with the two Ultras. I occasionally ponder going smaller (SB13 Ultra or Hsu ULS, etc.) for more placement options. Good luck with the tinkering and report back your finndings.
Why do all of my threads suck? Is there an internet posting school somewhere? -wes k