^^^^ ya, thats if you change the screws on the side... if you mean the tiny little set screws on the top, two to each saddle, then that just changes your action and will barely noticeabley affect your intonation. you can adjust the height to your liking (as long as the strigns dont BUZZ cus they are too low)
but ya if you turned the screws on the side, thats the intonation.. think of it this way
the string's pitch is determined by its length, it's width, and how tightly it's strung.
if you adjust the length of the string (altho however minutely) you shift the points where the notes appear along the length of ths string. you need to measure half way (the 12th fret) and tune it so that the 12th fret is the same pitch but an octave higher as the string. it's not as simple as tuning it, shifting the point and your done, because each time you shift the locations of the notes alnog the string, the entire pitch of the string changes as the length and tension both change.
it's hard, but if you have an electric tuner you need to tune the string, then play the 12th fret. (a natural harmonic right above the 12th fret is better, but im assuming you dont know what that is) find out how much higher or lower than the first note the 12th is, turn the screw a little (tighten the screw to lengthen the string, thus bring the note "closer" to the bridge. this will shift the pitch while raising the tension. retune the string, play the 12th fret (or harmonic) and repeat until they are both exactly on the note (0 cents off either way)
