Selecting your instrument also calculates the bridge position for proper intonation.
Notes on fret layout
The most accurate way to lay out your scale is making all measurements from the nut (using the "fret to fret" distance only to confirm your layout). Laying out frets only by measuring fret to fret will compound error. For example, if you're laying out frets by marking with a scribe and your accuracy is ± (plus or minus) 0.020", you could be off by as much as 1/4" at the 12th fret.
Measurements are given from the end of the fingerboard (face of the nut) to the center of a fret slot.