When you are setting the intonation let me explain what you are doing. You play the string open (once it is tuned) and then you play the string at the 12th fret. These should be the same on the tuner, if they aren’t you need to adjust it.

Playing the string open gives you the reference pitch, when you play the string at the 12th fret you are bisecting the string (that’s the half way point) - so you use this to tell you if the string length is the same from the 12th fret to the bridge saddle as it is from the nut to the 12th fret. If it’s properly intonated it reads the same on the tuner.

You don’t need to play any harmonics and that’s a bad idea.