Well, here's what I do (it works every time for me) -

First of all, make sure you have all reverb and effects turned off on your amp. You want a plain old clean tone. Tune the high E string with your tuner, and then put your tuner back in your case, cause you won't be needing it anymore. Tune the 12th fret natural harmonic on the B string to the 7th fret high E. Tune the 12th fret harmonic on the G string to the 3rd fret high E. Tune the 12th fret harmonic on the D string to the 3rd fret B string. Tune the 12th fret harmonic on the A string to the 2nd fret G string. And tune the 12th fret harmonic low E to the 2nd fret D string. Double check with a few chords, and you're done.