i assume this guitar has string saddles that are adjustable? if so... what you're going to want to do is tune the guitar to standard tuning. for example tune the bottom string to standard E. next you're going to fret the guitar at the 12th fret and see whether the note is flat or sharp. if the note is flat you need to move the saddle toward the nut. if the note is sharp you need to move the saddle away from the nut. after you make the saddle adjust retune the string to standard E. fret the 12th fret and check to see if it's flat or sharp again. if so, adjust accordingly. continue this process until your tuning of the open string matches (or closely matches) the fretted 12th string. The concept is that you're lengthening the string to compensate for the scale of your neck and the string correlation with where the fret wire fall along the strings lenght. now, not every guitar is perfectly manufactured and you might find that no matter how many times your try you can't get all strings exactly intonated... this is because the fret wires are straight accross the fret board and don't completely account for the delineated nodes along the string that produce the specfic note....
moral, it's not going to be perfect on every string and most ears won't know the difference but a good accurate-as-possible intonation can make a huge difference to a guitar players ear.
also, anytime you change string guage, bridge height, nuts... etc, etc... you will need to re intonate the guitar. these changes will alter the distance between the nut and the saddle and consequently alter the intonation.
NOTE: the adjustments to the saddles should be slight. a large adjustment will make a huuuuge difference. so start with small adjustments until you get a feel for how for you'll need to go to get the change needed.
