If your saddles are correct and the frets have a good crown on them and your strings are good then all you need to do is tune the E A D B E straight up on your tuner and temper the G string a little flat, working with it until a C chord and an E chord sound decent to you.
Remember that the guitar is a tempered instrument and does not play perfectly in tune, only close. There are other factors that will cause intonation problems, flat frets, defective strings, bridge saddles improperly adjusted, ecessive finger pressure etc. Make sure you have all that taken care of.