Noloft,
In the player, basically no BM. Set the speakers to Large and SW to Yes. Set all distances to the same distances, or '0' for best results.
You calibrate the LFE only sub using the player's calibration tone and the player's SW level setting.
Your player may have a global LP filter on the LFE output (check your manual). You can use the filter that's on the subwoofer's plate amp and dial any setting you prefer if your player has no global SW filter. If it does have one, it's probably high enough (120-150 Hz) to allow for a lower setting on your sub's filter (75-90 Hz).
As far as controlling the LFE sub's volume, you can either change it in the player's menu or manually at the sub's amp.
One of the distinct advantages to this system is knowing if and when there is any .1 content. You'll become accustomed to it's use in different formats for the first time, because with the summed signal system, all bass is played through the sub(s) and you just can't know which is which.
I've come to the conclusion that calibrating LFE is completely dependent on the room and the capabilities of a given sub and format. As you play with this set up, you'll learn to preset the LFE sub's level according to format and listening level before you pop in the disc.
The only potential problem is one of phase alignment between the 2 subs. Adjust the redirected bass sub 1st to be sure it's properly aligned with your mains, then, using a Hi-Rez MC disc that uses the .1 channel as a boost channel, align the LFE sub to the RB sub.
DVD soundtrack: Heavy LFE use.
CD music program: No LFE sub use.
SACD/DVD-A MC: Wildly differing .1 channel use, mostly as a boost channel, sometimes as a height, or full range channel and sometimes no use at all (even though all of those discs will say 5.1).
An interesting tidbit: The new Spyro-Gyra MC SACDisc, 'The Deep End', Track #3, has a low drone in the intro that's strictly in the .1 sub, and a sliding pulse on the 4, every other bar that's stricly in the RB sub.
I measured IMD with a single summed signal into the 2 subs, then with seperate discrete subs, both volume leveled, using extremely accurate equipment. The results were as predicted. It's funny to me how many, many people have told me that there is no advantage. They are all folks who've never tried the scheme. To me, it's instantly audible, but that's because my ears have become conditioned to the differences through many tests.
I love the big, clean subsonic sub for LFEffects, but hate that sub for music. Coversely, the music sub just can't cut movie sound tracks.
I think the intro of Blue Ray, etc., formats will add to those differences.
Sorry for the long version answer...