Cam, yes the subwoofer bass assignment should generally be set to LFE, not the "+ Mains" setting. This allows the sub alone to play what it does best, i.e., any LFE that may be present at times during movies, plus the redirected low bass in music from speakers set "small". In playing 2-channel CDs, the sub set LFE will get the redirected bass from the mains or other speakers when they're set "small" and the mode is set "stereo"(or a setting such as DPLII), not "direct", "pure" or any such setting that doesn't allow bass management.
On the use of Audyssey, yes your 3808 sets both the calibration numbers(level, size, distance, crossover)and room equalization. But as Andrew(Murph)pointed out, on p.43 of your manual it explains the choices that you have later in regard to the equalization part. You can either stay with the regular Audyssey curve that it set, choose Audyssey "flat"(most think that it emphasizes the highs too much), choose to set a limited number of frequency points manually(this is instead of the Audyssey setting, not a "tweaking" of it)or choose no equalization. You can experiment to determine which of the four equalization settings that you like best.
