Yeah intonating is a hassle!! I asked a technician once how to do it and he explained. It took me like 4 hrs to get everything set but I haven't had to intonated it since. Here's what I did, download a guitar tuner software program off the net that gives you the freguency at which your string is ringing at. That is a must, a regular little pocket tuner isn't enough. Also look up what each string's freq. responce would be.
To start you tune one string at a time. Once the string is in tune, play the 12th fret. It should be double the number as it would be for an open string. If an open string read 440 hz then the 12 fret should read 880 hz. It will never read exactly cause it will fluctuate, but get it as close as you possibly can. You do this by adjusting the bridge. Once that is done check the 5th fret, it should equal the freq. of the string below (remember tuning: 5th fret, open string). If it doesn't you need to do some more adjusting, and once you have the open and 12th strings in tune, and the 5th fret reading the frequency of the string below, that string is done. Go on until you have all your strings in tune. Hopefully you can find someone to do this for you cause it is a B#tch. Good Luck otherwise.
Depending on how well you take care of your guitar, or if you ever change strings (brand or gauge), or change the tuning of your guitar. You probably won't have to re-intonate. This is a pretty fail safe method (not perfect). So if something does slip out, re-adjusting open string and 5th fret should be all you have to do. The 12-fret is just to make sure the string is long enough so each fret hits the string where it needs to. Alot of people only do open and 12th, results will vary and most of the time the string will be in tune with itself. But not with the other strings which is why you should check the 5th fret also. It's an excellent extra precaution.
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