Well, height differences won't effect the intonation as much moving the saddles forwards or backwards will.
There are guides to know roughly how high each saddle should be, dependinng on the guitar's neck radius, which you can find online with a search (I don't have the figures in memory). But the way I set them is just by what feels right, according to the action and curvature of the fretboard.
As far as intonaiton goes, get yourself a tuner and do a search on how to set that, too. It's really not difficult. :)
