[Stratrat]

It sounds like you're talking about setting intonation. Yes, it's done with a tuner - the more accurate the tuner, the more accurate the results. If you Google "guitar intonation" or something similar, you should come up with plenty of tips and how-to information to help you out. It's really pretty simple.

Note that "intonation" is not the same as "tuning", per se. A very simple explanation would be that "tuning" is what will make your guitar sound right when you play notes/chords...."intonation" is what will make those notes sound the same up and down the neck (i.e. not flat or sharp in different locations on the neck.) If your guitar is in tune, your open strings will be E-A-D-G-B-E.....if your intonation is set correctly, an 'E' at the 12th fret will still register on your tuner as an 'E' - not Eb or E#.