Ok. Tune your guitar up all nice and good. Turn on your tuner. Play a harmonic at the 12th fret on the low E string. It should be somewhere in the general vicinity of dead-on. Now fret the low E at the 12th. Chances are it's either gonna be a little sharp or flat of whatever the harmonic was. If it's flat, you need to move the little string-holder thing (saddle? Is that what they're called?) of the E string forward towards the neck. If it's sharp, move it farther away from the neck. Now check both the harmonic and fretted note again to see if they're tuned to the same place. If not, just make another adjustment. Keep doing this until the fretted note and harmonic are one and the same. Now do this for the other 5 strings.

To help you remember, just think of the 3 F's: If the Fretted note is Flat, move it Forward.

I hope that helps.