Assuming your frets are cut right and your bridge is positioned correctly, you should only need fine tuning in the intonation. I beleive a quick way to check your intonation is to fret the 12th fret, and then play the 12th fret harmonic, and they should be the same. I dont think anyone really checks every single note on every string to make sure they are all in tune. From my understanding, if your 12th fret is in tune, and your open is in tune, then you should be in good shape as long as your frets are good. Someone please correct me if i am wrong.. im quite a novice