What is the absolute fool proof and proper way to set intonation?
The way I've always done it is to play a harmonic at the 12th fret and then tune it to the exact same pitch as the open string.
Is that the correct way or should I be tuning the open string to the 12th note fretted?

If you're tuning an open note to a fretted note, how do you set the intonation properly when a slight difference in pressure can make the fretted note go sharp?