In an AVR, when all the speakers are set to Large, the crossover setting may still affect the LFE channel's response. I suspect a new design like the 8801 will not do that, so it does not matter, as the LFE path bypasses the crossover. That's why some AVRs/processor offer a separate "LFE low-pass filter" in case one desires to tailor the LFE rolloff. IIRC the 8801 has that, and you still get to make that decision (do not set it lower than 80 Hz, but you can set it higher than 120 Hz since the REL has a 4th-order 120 Hz LPF). I like my LFE cut off at 80 Hz since I also play 5.1 music, and it needs it there.
In your case, you are using the 8801 bass management to cross over the surround speakers, so those should be set small and the 8801 crossover chosen accordingly (or left as Audyssey decided). If Audyssey decided your fronts were Small, setting them to Large for the REL might lead to interesting results since Audyssey may not be doing the optimal thing for the EQ below the corner it recommended. It has been said one can raise the corner, but not lower it, but I'm not sure of the implications. That's best resolved at the Audyssey thread.
In the REL, the high level inputs are affected by its "crossover" [sic] control (it's a LPF), which you use to get the best blend between the full range mains and the sub. The LFE input is not affected by the "crossover" filter, but is always capable of 120 Hz BW as it has a separate filter for that.