Dave,
I have a similar speaker set up. Glad to hear you are solving some of your problems, there should be no lack of bass with that set up!
What I have found best for my room and system is:
BP7000SC - set to large hooked up via speaker wire, LFE connection doesn't seem to make a difference and is just another 2 cables. These speakers are flat +/- 3db to 20Hz and SHOULD be run as large.
3000 center - tried both large setting and small with a 40Hz cutoff, both work well there doesn't seem to be a ton of <40Hz center material, and it is nice when deep villian voices emanate from the center channel.
I have 7001SC for surrounds and also run them large, for you however I would think 80Hz would work well for the BPVXs. That built in 6.5 sub would be better off handling only upper bass, crossed to the subs.
As you have discovered experimenting with sub position is the only way to truly unlock what those reference cubes are capable of. I place my two subs along the mid-points of my side walls, by far the best location.
One of the most powerful tools for setting definitive super towers bass level IMO is the old avia DVD. In the sub-evaluation menu it will run alternating high and low frequency to any channel set as large. With a basic SPL meter you can tailor adjust each built in subs level to exactly match the mid-high frequency output of that same channel. Using this method in my room each built in has a different level to achieve the same SPL even though it is a perfect rectangle (all subs are between 10 O'Clock and noon).
Enjoy that system! There is no reason with experimenting of positioning and settings you should be able to knock the socks off of anyone who sets foot in that room
135" screen doesn't hurt!
