I don't think it matters whether you run "stereo" signals to the subs or not, if the low-pass filter is set down around 35 Hz. Very, very few recordings have stereo bass below 80 Hz, much less down at 35 Hz.
My suggestion would be to set the volume level of one sub (preferably the one that will be getting the most boundary reinforcement) with only one main speaker playing, then duplicate that volume setting for the other sub. This would be a starting point; from here, go back to both main speakers playing and adjust both subs together to fine-tune the overall level. I figure that if both subs are at the same output level, their tendency to sum to a smoother overall response will be maximized.
My understanding of how to apply Geddes' recommendations to this situation would be to set the level of one sub first (the one that will be getting the most boundary reinforcement), with both main speakers playing, then turn up the other sub just enough so that it improves (smoothes) the first sub without making the bass too loud. Geddes also recommends using a different low-pass filter frequency setting for the subs.
As an alternative, if you have one sub over on the left-hand side of the room and the other over on the right-hand side, along the sidewalls but not equidistant from the listening position, you might try running one of them out-of-phase with the other. Or, if the subs have continuously-variable phase controls, run one of the 90 degrees shifted relative to the other. The latter would be a David Griesinger type setup; the former a pooman's Griesinger setup. The idea is to synthesize an inter-aural phase difference in the deep bass, because the ear/brain system will interpret this as spaciousness and envelopment.
Duke