Definitely looking to be an interesting setup. So...

Set up the SMS-1 using an 80Hz crossover so that you have the sub response flattened up to 80Hz (the upper limit that it's likely to be dealing with). Then go through and adjust the presets.

Preset 1: SMS-1 crossover set to somewhere around 50Hz and probably 24dB slope, no contour applied, used for two-channel with the stereo pre-amp (using the second set of outputs from the stereo pre-amp, with the first set going to the amp and on to the mains).

Preset 2: SMS-1 crossover set to 80Hz and probably 24db slope, no contour applied, used for high-res audio (DVD-Audio/SACD).

Preset 6: SMS-1 bypassed entirely, Denon 4806 doing its own thing for DD and DTS sources. The only thing I might suggest would be leaving the SMS-1 in the loop and (after calibration) run the Audyssey. True, you wouldn't be able to tell the Audyssey to limit itself to above 80Hz, but it's going to be listening to its test tones through the SMS-1 and therefore should see no need to adjust anything in the SMS-1's realm once you've dialed it in. It'd be easy to test, at least: run the Audyssey setup with the SMS-1 on preset 4 (the default preset, which has no contour applied) and on preset 6 to see if preset 4 gives it any trouble.

As for the final question, I'd probably lean toward your first approach (summing the pre-amp outputs into a single connection and then letting the SMS-1 sum that in with the Denon's LFE output). I think the SMS-1's unbalanced and balanced inputs and outputs are shared (I did test that the balanced input reaches the unbalanced output, at least), which would let the second approach work, but I'm not certain of it.