I can only speak from my Audyssey/Marantz experience, but I can adjust each sub individually, as well as both as a pair.
This is why I summoned ADTG... he knows Yammies and hopefully MA (as he's a dealer.
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Trying to treat each Sub on its own, once the responses have been "corrected", is usually the wrong approach. You have to think of them now as a single unit.
And while I can adjust levels independently, as I said, I also have the combined response which I can adjust as well, without defeating my room correction (rather working within it's adjustment parameters).
Does that make sense?