It will treat that output as having one sub connected. It will not be able to take those as a separate connection to two subs, that is beyond it's built in capabilities as it is designed for one sub from each LFE output.
About Audyssey Sub EQ HT™
Audyssey Sub EQ HT™ makes the integration of dual subwoofers seamless by first compensating for any level and delay differences between the two subwoofers and then applying Audyssey MultEQ® XT32 to both subwoofers together.
To run Audyssey Sub EQ HT™ you must select “Measure (2 spkrs)” in “Channel Select”.
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