Yeah I'd get rid of the double bass via LFE+Main also. The 120 LPF of LFE is not a crossover, but is the usual setting for such (just limits the content in the LFE channel, which is normally 120hz anyways). You should disable the crossover on the sub (probably only a low pass filter anyways) and let your avr do the bass management, altho some subs with an LFE input do that automatically. Your crossover between speaker and sub (for redirection of bass frequencies in other than the LFE channel) is the 100hz you have it set at. Phase at 0 is a good start but compare flipping it to 180 to see what yields stronger bass with your sub's location. Gain setting on the sub is a way of matching your pre-out level of the avr to the sub amp's sensitivity level, but I'd recommend sub trim levels in the negative range also rather than in the positive. If the sub trim level in the avr was set to +8 then I'd raise the gain level on the sub until it drops into the negative range on another run of Audyssey....
Did you start of with a determination of best location of the sub with a sub crawl?