In general, the LFE input bypasses the subs internal low pass crossover. Even if the frequency is turned all the way up, this input should be superior if you are using the AVR to select the crossover frequency (which I'm sure you are). I believe that the LFE input also corrects for the 10dB boost needed for surround decoding (other correct me if I'm wrong). The R / L are just there for stereo input and use with legacy equipment that didn't have an LFE output.
Since the signal is split inside the AVR, it shouldn't matter if you use one output and split it further away - this would just be a matter of convenience. If the two subs were in opposite directions, I would use both outputs. If in the same direction, I would use one cable to the first sub, split the signal there, and run another cable to the second sub.
2-Ch (HT L/R): Oppo BDP-105 BD, Adcom GFP-750 pre, Bryston 10B Sub Xover, Bryston 4BSST2 / Paradigm Signature S4 v.2 (L/R), (2) SVS SB12-NSD (Subs)
Home Theater: Bryston 4BSST2 amp / Paradigm CC-590 (C), Outlaw 7700 amp / (4) Def Tech UIW-RSSII (LS/RS/LB/RB), Samsung 46” 3D LCD