in theory, if you have lines, intonate so that stopping the note with the edge of your finger right on the line is in tune.
same with side dots, although it might change from one brand to the next, with a doubled pair of dots at the 12th being equidistant from the virtual fret (so you'd want the edge of your finger to be right in the middle) or set up so that the second dot is right at the 12th, so you'd want the edge of your finger to be there.
in reality, you get it in the ballpark, and so that the same position is in tune for all 4 strings, and the rest you just do by ear while playing.
Guitar Repair Gnome
Alpha Music, VA Beach