Re: guitar intonation
do it open then fretted.....open and 12th harmonic will give you slightly different notes.
The purpose of intonation is for you to have the same pitch open as fretted for each string at the 12th fret-the 12th fret is right in the middle of the 2 octaves on guitar so you'll have the best average intonation throughout the guitar.
A few tips-the strat was designed to have a slight relief arch in the neck for best action and intonation.
play each string open, and try to match them with the 12th fret FRETTED and you'll get good results!