
The lower portion of the guitar body, aligns at the 22nd fret and the top portion aligns at the 19th fret. Opinions may vary. Do your research, examine other guitars and get it right the first time.
Note: The drilled hole in lower portion of the neck body is for positioning of the bridge. The distance from the 12 fret to this hole is exactly (or should be) the same distance as the nut to the 12th fret. The closer you get this, the better your intonation will be. To ensure accuracy, I measure the distance from the 12th fret to the bridge saddles. This is a Carvin neck and if you use a Carvin bridge, the middle screw hole of the bridge when aligned with this hole, will center the bridge but be sure to check for accuracy. Run a string from the center of the nut, down the length of the neck and center the other end of the string over the center of the bridge. Trust but verify.
Note that in the next image I use a frame from a cut out body to give me straight edges to clamp with. This frame was cut from a guitar that I built back in '93 using a CNC router and is very clean.

I let the guitar setup overnight and after removing the clamps, I get to work routing out the cavities for the pickups and the wiring.