You can do stereo subs or mono (LFE) subs... your choice. For a home theater I would go with the mono or .1 setup, for a strictly music system I guess you could use the stereo configuration.
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If there is no designated LFE sub, then the LFE signal will be distributed across all front and rear subs.
With front and rear pairs of subs, the bass from the front and rear speakers will be directed to the respective pairs of subs, so the effect is to make your front left/right and your rear surround left/right more full range, and improve left/right and front/rear effects. The cutoff that redirects lower frequencies to the sub instead of to the main channel is determined by the size you tell RP when you set up your system.
Generally, 4 subs (2 pairs) will balance your bass better in a room, so you get more consistent performance in the room - fewer peaks and nulls. As well as the improved directionality.