When your intonation needs adjusting, first engage the tremolo stop.
1) Once the tremolo stop is engaged, tune your guitar to an electronic tuner. Now, check the intonation of one of the strings to see if the intonation is sharp or flat by chiming the string over the 12th fret.
2) Now fret the string on the 12th fret to see if the pitch of the chimed note matches the pitch of the fretted note.
If the fretted note pitch is lower than the tuned pitch of the chimed note, this means the intonation is flat. If the fretted note pitch is higher than the tuned pitch of the chimed note, this means the intonation is sharp.
3) To adjust the intonation, first remove the string tension by unlatching its quick release saddle as if you were going to remove the string
4) Then, using a 2.5mm Allen-wrench loosen the saddle hold-down screw while holding the saddle in place.
Be careful not to let the saddle move when you release the hold-down screw. Now carefully move the saddle in the desired direction. Move the saddle toward the pickups if your intonation was flat or away from the pickups if the intonation was sharp.
5) Carefully re-tighten the saddle hold down screw. Re-latch the string and tune the string back to the previous pitch using the range-tuner set screw, not the fine tuners, then check the intonation and repeat the above procedure on all the strings as needed.