Thanks, SaguaroGeorge, for asking your question. My situation is something like yours - same listening tastes but my Magneplanar 1.6QRs get down to about 40Hz. What I want subs for, if anything, is to reproduce all the content in stereo or multichannel musical material, including organ pedals and room acoustics. From what I've read two subwoofers allow better handling of reverb modes in the listening room, as well as two small boxes possibly being easier to integrate visually than one big one.
I'm pretty sure the answer to your "finally" question will be "via the pre-out" if it's one sub, but to preserve the stereo difference signal (slight though it may be in the deep bass) . . . I wonder if you'd have to send the two pre-out signals to the crossovers on the two subs, then send the high-pass-filtered outputs of those crossovers back to your power amps. More cable unfortunately, but you'd have a fully biamped system, with the two channels on each side being the low bass and everything else.
Knowledgeable people, the ball's in your court.