Over the last several years we have sold/installed many different brands HT systems using (2) subwoofers...
Though each brand have products that have (2) subwoofer outputs the majority are simply wiring the (2) subwoofers in parallel...
IMHO..
EQ for multiple subwoofers is a very complex procedure, by far the best EQ software we have found for this was the SW developed by Harman & Dr.Toole's R&D team. This was implemented in certain HK, Lexicon and JBL Synthesis processors & AVRs. The SW would sweep each subwoofer and adjust each independendly for phase, level & frequency and then merge these together accordingly. Since the subwoofers low frequency performance are crucial for the HT system soundstage, 1 should be prepared to try various subwoofer locations to achieve the best final results. 1 reason I think the Harman SW was the best is that it was developed/programmed by acoustic engineers rather than electronic hardware engineers who had incredible background acoustic system design experiences from JBL both from the pro and consumer biz.
A crucial point is to use the same brand/model subwoofers for these system, if one wants more technical info google multiple subwoofer white papers by Dr.Toole, Dr.Olive, Todd Welti. Note that this team has been working with multiple subwoofers for >18 years...
Just my $0.02...