This is really more of a bass management issue.
I assume your AVR is Dolby Digital or DD/DTS. If you set all your speaks to small and the sub to on/yes, the AVR sub pre-out will send the LFE channel, and the redirected (i.e., below the xo in the AVR BM circuit) bass for each channel.
If you set the speaks to large and the sub to on/yes, then the sub pre-out only sends the LFE channel.
If you set the speaks to large and the sub to no/off, then the LFE channel gets redirected to the L/R fronts, and the sub pre-out sends nothing.
So figure out what you want to send the subwoofer, set the BM menu accordingly, and just connect the sub pre-out to the L or R low level connection on the sub amp.
If the sub amp has a low pass filter, set it to the highest frequency setting (or disable it if there is a switch) to avoid cascading it with the AVR LPF.
Then calibrate and balance all the speaks (including the sub) with an SPL meter and a disc like Avia. HTH.
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