I am building a few neck throughs now.
Lay the neck blank down on the bench so the grain is running parallel to the bench. Now you draw a straight line on the side of the wood that is facing up. This will be the line designating the top of the body. Now we need to draw the neck angle
You need to decide what the scale length of the finger board is or you won’t know where to start the neck angle from. So, you need to get your finger board and lay it down on the block of wood and mark where the nut starts and where the 12th fret hits and where the 16th fret hits. Then take a yard stick and measure from the end of the board starting at the nut to the 12th fret. Then you take that same measurement and run it from the 12th fret to where the bridge will be located. That is the scale length and where that measurement hits at the body, is where the E saddle of the bridge should hit.
After you have all these lines marked you can start laying out the proper angles.
Neck drop for T.O.M bridge. From 16th to front of nut. 5/8" drop.
Neck drop for Badass bridge. From 16th to front of nut. 11/16" drop.
Neck drop for Recessed Floyd Rose bridge. From 16th to front of nut. 1/2" drop.
Head drop for all of them. From the back of nut out 7". 1 3/8" drop.
For the frets past the 16th fret I use a shim that I get from the drop off of cutting the neck angle from 16th fret forward. Just cut it a bit longer than what youll need to complete the fretboard so you can just cut that off once you have the fretboard glued down.
Front of nut is the side of the nut closest to the fretboard, back of nut is the headstock side of the nut.
EDIT:The measurements are from Neal Moser's site, as is the method on how to get the angles.