I get asked quite often about how I figure out where to put the frets on my instruments. Building proper guitars takes incredibly precise measurements, the length of the neck and the height of the nut and all sorts of different factors go into measuring the exact placement of guitar frets.
My stuff tends to be much harder to accurately measure distances and figure out heights and how much a neck will bend under tension. So, over the years, I've realised that the best way to do it with oddball instruments like mine, is thusly:
Frets are the last thing I do to my instruments.
I string them up, tune them, leave them for a day or two and tune them again. Sometimes the strings need to stretch out a bit or the neck needs to settle down for the winter, so it's good to take your time at that bit.
The next step is to take whatever you're using for your frets (I tend to favour round nails at the moment) and to simply plug in your tuner and go up and down your neck with your loose fret on the neckboard, pushing the strings against it until you hit an in-tune place. Mark it with a pencil and keep going up until you hit the next note.
The video should clarify what I mean if that doesn't make sense.
Be patient and slow while trying to find the right spot, my tuner is good but often gets confused and jumpy. Also, it REALLY helps if your nut and bridge are exactly 90 degrees to the neck, this way your frets will be more consistent if they're all at 90 degrees also.
If you want to do the measurement methods, the best calculator I've found has been here: http://www.manchesterguitartech.co.uk/fret-and-nut-calculators/