You could run a 1Hz sine wave at just enough level to see the woofers move and confirm if they are moving in sync. Some sound cards however filter out before that so depending on the card this will/won't work but something like that really is the most definitive as far as woofers go anyway. You don't even really need to see it well, I've been known to do this test and just place my fingers on the woofers and be able to tell if they are in phase.
For example my RME will go all the way down to DC so the test would work but all sound cards don't do that.
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