There's really no such thing as 100% phase alignment on multi-mic'd sources. Say you've got a drum kit with an XY overhead pair and some spot mics. In a typical setup, the snare transient
will hit the snare mic before it hits the overheads, and bingo, you have non-alignment. You could decide to slide the snare to co-incide with the snare transients on the overheads, or vice versa, but then some other element will be non-aligned.
Better than thinking about "correct", IMO, is thinking about "good". You
will have non-alignments, and some of them will create horrible cancellation, some of them will be unnoticeable, and occasionally, some of them will be kind of cool. And this stuff is all best solved with your mic placement, I reckon.