I searched on this thinking it must have come up before, but I may not be using the right work combo.
After changing strings I always put the bridge back "about" where it was, using the "footprints" on the top, and the nicks in the F-holes as reference. Then I tune the G strings and the E strings. I check to see if the harmonic is over the 12th fret, and make minor adjustments to make sure that the harmonic is strongest directly over the fret.
I finish tuning and that is that.
All of this is a bit inexact. I was wondering if anyone has a more exact way of doing this, that doesn't require special tools.