One thing that helps is to remember that there are 100 cents in a tempered semitone. The distance from the nut to the first fret represents 100 cents.
If you're trying to get the fretted note at the 12th fret to be exactly on octave above the open pitch, it would seem to me that you'd look at the distance between the 12th and 13th frets, since what you're trying to do is knock (in your example) 10 cents off the fretted note pitch. If that distance is about 16mm, then 1.6mm will be pretty close to ten cents worth, and that's how far you need to move the saddle. If it's sharp, move the saddle back.
This is an approximation, of course. In such cases I try to do two things. One is to find some way of making a temporary change that you can reverse easily. That may not be possible in this case. When setting a new guitar up you can start with a flat saddle top and put a piece of string across it under the string you're checking as a stop point. Moving the stop back and forth makes it easy to find the right length, and you can then file the saddle top to match.
Another thing to do is remember the 'Rule of Half': make only half the change you think you'll need, and see how that works. Sometimes you get it right the first time that way, and it saves you from going too far. At worst, you just have to go in and make another adjustment.
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