By the way, will this be a steel string guitar? Because it will have to have a compensated bridge saddle on it to intonate properly when a note is fretted... IOW is the bass side of the saddle slanted away from the nut about 1/8 " or so out of parallel (to the nut) The thicker bass strings need more length because they are less "resistant" to tension before going sharp, as you will know from having tuned the guitar--it takes less of a turn on the bass strings to raise the pitch by a half step, than on the high strings.

But whether it is a steel string or classical (nylon string), it will still have to have some compensation allowed for in the bridge placement. And this is very picky and tricky. As mentioned above, if you want a certain scale length, (say 25 inches) halve that (12.5 inches) and that is the placement of the 12th fret. Then you can layout the reast of the frets from there, but the distance from the twelfth fret to the bridge saddle should have a little more added to it for more compensation. Luthier William Cumpiano suggests .15 inch for steel string guitars and .1 inch for classicals. That's if you want the thing to be able to play in tune at all.