The tricky art of intonating a guitar.
First you should know the list of things that can affect the intonation.
#1. Are you using a different gauge of strings than usual?
#2. Are you using a different tuning than usual?
#3. Have you recently changed the height of your pickups?
#4. What condition are your frets in?
All of these things can effect the intonation of your guitar.
#1, 2, and 3 are no problem because we can intonate our guitar around these specifications but if our frets are worn out, intonating our guitar will not help.
When intonating, we are making sure that the string is the right length from the nut to the saddles so that each fret creates the correct note.
The way we test this is to match up the 12th fret harmonic to the 12th fretted note. The 12th fret harmonic is seen as being correct so the focus is to make sure the fretted note matches. If they are the same then everything is set.
If the fretted note is too high then the string lenth is too short so we'll have to lengthen the distance of the saddle to the nut. If the fretted note is too low then it's just the opposite.