audioseeker,
It depends on the receiver, but many receivers allow you to select either YES or PLUS subwoofer modes (these names differ from brand to brand). In YES mode, the sub receives the LFE channel plus the low-pass signals taken only from the channels that are set to SMALL. The sub does not receive any signal from the channels that are set to LARGE.
In contrast, in PLUS mode, the sub will play the LFE in addition to low-pass signals from all channels, regardless of whether they are set to SMALL or LARGE. You are correct that the PLUS mode can cause a phase-related problem (comb filtering) between the identical bass sound coming simultaneously from the LARGE front channels and the sub.
In the end, the best way is to experiment with all of these configurations, and pick the setting that sounds best. But the subwoofer set to YES at 80Hz, with all main channels set to SMALL, would be a good starting point (in fact, this is the setup recommended by THX).
