abt
BT
dont you have to move the saddle forword if you are sharp?? also heavier strings are definatley in order, and dont fret the string to check intonation its way to unreliable always use the harmonic.
Do NOT use the harmonic! If you check against the harmonic at the 12th fret it will always be right because the harmonic won't ring out otherwise. The harmonics don't care about where the frets are. The 12th fret harmonic needs to be the same as the open string and the 12th fret.
The location of the frets is a compromise, there is no such thing as a perfectly intonated guitar. That's why you have adjustable saddles to try and create a workable string length in relation to the frets.
The easiest way to do this is to tune the open string using a tuner then fret the 12th fret, it should be the same. If the 12th fret is sharp move the saddle forward, if it's flat move it back.
EDIT:
This explains it better the me: http://www.icepoint.com/guitar/Setting up your electric guitar/index.htm