In a somewhat smaller room I have one Velodyne DD-15 and VSM-MX/BBAM with line-level connections to the sub from a BAT VK5i tube amp. Since the BBAM filters all bass below 28hz, using speaker-level outputs from the amp to the sub is not appropriate. You might need two subs in a room as large as yours. Corner placement is usually best with a single sub; if two subs, try one just outside each main speaker. With the Velodyne DD, two subs can be daisy-chained and controlled from one remote. In an irregular room such as yours, it might be best to identify optimal room positioning by putting the sub in the listening position, and moving the sub microphone around the room to the point where the microphone produces the most linear frequency trace on the spectrum analyzer. Then switch the sub and mike positons. If the floors or walls vibrate, try the sub on a platform such as Auralex Gramma.
With the Merlins I use a low crossover at 30hz with 12db slope. If due to large room size you're already getting weak bass response from the Merlins, you might want to cross over a little higher or play with the parametric equalizer to notch up sub output around select higher frequencies. With the DD parametric equalizer I was able to integrate bass with the Merlins +/- 2db from 15hz to 100hz.
At such a low crossover point, it will be time consuming to optimize any sub by ear. Get a sub with an integrated frequency analyzer and digital equalizer such as the DD or Thiel. Given the right set-up tools I think you'll find that differences between various hi-end subs is subtle in comparison to the differences between hi-end main speakers.
Dave