http://www.guitartricks.com/forum/showthread.php?t=30375
The basic intonation is to adjust the saddle so that the open string and fretted at the 12th are coming out the same on your tuner.
The guitar should be in tune to start.
Begin with the E string (I always start with the high E) and do one string at a time.
If it's sharp at the 12th, move the saddle back (lengthen the string). If it's flat, move it forward. Loosen the tension on the string to move the saddle, then tune back up to pitch to see the result of your adjustment. Rinse and repeat, as they say.
...so ever since then, I always hang on to the buckle.
