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It's frustrating and slow going the first few times you do this, but after a while saddle adjustments will feel no bigger than tuning knob adjustments to you. Re-tune the harmonic and repeat until both the harmonic and the fretted note are perfectly in tune for their whole sustain. If that note is sharp/flat, move that string's saddle towards the body/neck of the guitar, respectively, using the saddle screws. You can do this by tuning the 12th fret harmonic perfectly, then fretting the string at the 12th fret and playing. Also, PLEASE remember to check your intonation regularly - you can do the world's best tuning job, but if your bridge isn't set right you won't be able to appreciate it. It takes longer this way, but I've found the guitar seems to stay in tune longer once you're done.
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Then I repeat with all the other strings, come back around to the first string and keep repeating the process until every string is in tune for their whole sustain. If its wobbling, I usually adjust based on the direction it wobbles first. I don't move on to another string until that harmonic rings in tune for the whole duration of its sustain, including the attack. My method for using a tuner is to hit the 12th fret harmonic (always tune the harmonics) and let it ring. Tommy Emmanuel uses A441, but he's the only player I know of who does this. Firstly, make sure your tuner is calibrated to "A440" (this means the tuner will use the frequency 440Hz as its reference for the note "A").
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