Making your chords perfectly in tune up the neck is next to impossible. The guitar isn’t really set up to do that, but we can temper our tuning to facilitate better intonation up and down the fret board. I almost never take all my strings off at once, preferring to change them one at a time starting with the low E string. It might be superstition, because I know wood has a memory, but I don’t like to put the neck through that much trauma when all the tension is released.
After putting on a new set of strings, I check my intonation by playing a harmonic at the 12th fret of the G string and then fretting the note at the 12th fret of the same string. Using a tuner, I look for an exact match. But if the fretted note is sharp, my string is too “short,” meaning the distance from the nut to the 12th fret does not match the distance between the 12th fret and the saddle.
If that is the case, I get a screwdriver and adjust that saddle piece backwards (if possible) which on Stratocasters and most Gibson guitars means tightening the screw. If the 12th fret note is flat my string is too “long” so I move my saddle piece closer to the nut by loosening the screw.
Running this test on all 6 strings will set your intonation perfectly or as perfectly as possible on a guitar. I usually do this every other string change, because my guitars don’t drift too much. One more tip: When all is right with my intonation, I’ll usually tune my low E string very slightly flat. This makes my 3rd fret G right in tune, and since the low open E vibrates quite a bit, it seems to compensate and not sound flat. On some guitars I’ll even tune the high E string a little sharp, but that really depends on the instrument.
The better you play the more you’ll demand good intonation out of your instrument. If it doesn’t tune up…sell it!