Peter, you're correct that in general the setting that gives the stronger bass means that the sub and mains are in phase and it's the better setting. However, it's possible that due to some room resonance near the crossover point that the result would actually be better with the sub out of phase and partially cancelling the resonance. Especially if you have the sub in the corner, which is generally best, this isn't the usual result, but as always, experiment.

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Enjoy the music, not the equipment.