For setting a moveable bridge, set it so the distance from the 12th fret to the bridge is the same as the distance from the 12th fret to the nut. That will be approximately right. THEN--play the harmonic on the 6th string, 12th fret and compare it to the fretted note on the same string, 12th fret. If the fretted note is flat, move the bridge a hair closer to the 12th fret, if sharp, away. You can check it by ear, but an electronic tuner may be more precise.
Once the harmonic and the fretted note are identical, do the same thing on the 1st string (trying not to change the point where the 6th string contacts the bridge--or saddle). Once you've got it, recheck the 6th string. It will take some trial and error and a fair amount of fussing, but once both the 1st and 6th strings are accurate, all the other strings should be okay.
I've done this a fair number of times on the various guitars that new students have arrived with.