If your going to adjust your guitars action, (the height between the strings and the fretboard) do it now. If you set your intonation, and then adjust your action, you'll have to start all over again adjusting your intonation.
Tune your open strings on your tuner. Play the harmonic at the 12th fret of the first string (E). The harmonic is the absolute center between the nut and the bridge. The principal here is that when you actually PLAY the note at the 12th fret, it is also the absolute center just like the harmonic.
Hold the note down at the 12th fret and check it on the tuner. If it's dead on E your intonation for that string is good. If the note is FLAT it means the distance between the nut and the bridge is a little TOO LONG. So you have to adjust the bridge saddle to move it closer to the nut, in other words shortening the string length.
If the note is SHARP, it means the distance between the nut and the bridge is TOO SHORT.
So you may have to adjust the opposite direction (make the string longer). Once again, you may have to adjust a few times.
You will probably have to loosen the string in order to allow the saddle to move. Then retune and check the note at the 12th fret again. Repeat the process until you have a perfect E at the 12th fret. Then repeat the same process for each string. This requires some patience but it's worth it.
If particular frets are out and others are in, look to see if the frets are worn to the point where the string is not leaving from thier centers. If so, you may need to grind or polish or new frets correct the problem. Bad scales are not unusual on handmade or very cheaply made guitars. If the intonation starts out bad on the first few frets and gets better going up to the 12th fret, your guitar may have a misplaced nut. This will throw the entire scale off. So you may need to take your guitar to a pro shop so they can relocate the nut.
Guitar intonation adjustment is often very small so be careful until you've got the hang of it.
