thats the problem. If Audyssey doesn’t get the time alignment right, you’re completely screwed and there’s no way for you to fix it. If you manually time align the subs first with one sub out, you can let Audyssey do it’s thing with the EQ (seeing both subs as just one subwoofer) and speaker-sub alignment and if anything is messed up you can manually fix it.Like I said, I would try Audyssey first for the reasons I listed, and then go the other route if that doesn't work out. In some setups, that may be necessary.
Also, I'm not sure I would trust Audyssey to do the right thing if I presented it with already time-aligned subs - what if it messes it up? That is part of the problem. You need to get the automated part out of the way first.