Once you have the scale length, you need to know how many frets there are on the neck: is it 12 fret, 14 fret, or something else? If it's a 12 fret neck, then the _theoretical_ saddle position is exactly 1/2 of the scale length from the upper edge of the body. So, for your scale on, say, a 12-fret 000, the saddle would 'want' to be 12.3" from the edge if there were no compensation. I usually just go with this number, since my bridge plates are wide enough to allow for a fair amount of 'wiggle room'. You could easily enough factor in some reasonable amount of compensation and go from there.
If you're using a 14 fret neck, then you need to find out how far the 14th fret is from the nut, and subtract that from the scale length to get the distance from the body edge to the saddle. If you have the fretboard in hand you can measure it. If not, you can find a table of fret distances, or generate one using a spreadsheet or one of the fret calculators, and go from there. The program I wrote up does the subtraction automatically, and prints out both 'nut to fret' and 'fret to bridge' distances, which makes life easy in that respect.
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