The function of intonation setting up is to make sure your guitar play in tune. If your guitar has an intonation problem, even if you tune the open string according whatever electric tuner or other instruments, your guitar will not keep in tune when you press down the string on fretboard.
To check out if your guitar has an intonation problem, there is a simple way to do it. First, tune your guitar to standard pitch according to your reference pitch such as tuners or other guitars. Then lightly touch the string around the potion of 12th fret with your left hand finger, don’t press string down to fretboard, and pick the string with your right hand finger at the same time, then remove your left hand finger quickly. This is also called harmonic or chimed note. If your fret finger touches the right position of the string, you will get the harmonic or the chiming sound. Otherwise, you need to move your finger back and forth around the 12th fret to get the correct point. After you get the chime note, play the same string by press down it to the 12th fret, these two notes should be the same. If the 12th fret note is lower or higher in pitch than the harmonic, it is a sign that your guitar has intonation problem.
How to fix it? Guitar intonation setting up is little complicated. You’d better send your acoustic guitar to the local guitar repair store. In most case, the repairperson will use compensated saddle to fix it.