how long the fretboard is not important. nut to bridge is the measure that counts... got to http://www.stewmac.com/FretCalculator fill in the boxes and you get a table that give you fret positions.
Hint: input the measure in mm's, not inches. You will get back measures in mm's... use whole mm's, it's accurate enough and probably as close as you can measure. Also, measure/mark each fret from the bridge, not from the next closest fret which will only compound measuring errors....
that should get you going... oh, input something like 24 frets, even though you probably only have fretboard enough for 22...
that should get you started...
You can use an existing guitar & line the neck up but you'd have to use a guitar with the same exact scale (bridge to nut). But here is another way that I learned of.
Draw a line on a large piece of paper. The line should be the same distance as your particular scale. Then you divide that scale by the constant 17.817. Whatever you get, draw a line that long perpendicular to the beginning of your scale line. Then connect the two ends to make a long triangle. Take a compass with a pencil attached to it & starting with the beginning, swing it down to the base of your triangle. That is your first fret. Continue all the way down. The frets will get closer together because the compass will have to be made more narrow each time as you move further down the triangle. BTW, I think you use millimeters for the calculations but I could be wrong.