Drums microphones alignment techniques

Hi, I am getting ready to track/mix drums and I plan on using auto align to tighten up any phase/polarity issues from the session. I have a question on how the time adjustments are made:

Say I use the snare top as the reference, then I send that to an overhead mic and align them. Does autoalign move the snare back xx ms or does it move the overhead forward xx ms?

The same question applies for room mics. Lets say I want a mono room to be in phase with the snare but I want to keep the approximate time difference that already exists from the distant placing of the room mic. Will sending the snare as reference for the room make autoalign move the room mic up or delay the snare to match the room?

I read the multi microphone drum recommendations in the FAQ, and from what I understand auto align can either move a track forward or backwards to be in phase with the reference track, but I just wanted to make sure this is what is happening.

And to be clear, you reccomend aligning the kick drum and toms to the overhead after aligning the overheads to the snare? And i assume its user preference as to which overhead you align it to in a stereo pair?

I hope my question makes sense. Thank you.
Sam