OK, here goes.
First, I take the dimensions from the nut I plan to use. In this example case, it's a GraphTech PT-1200-00 4 string bass nut. From Graphtech's side, you can do a little math and see that the distance from the center of the outermost nut slots to the end of the nut is 5mm. You don't really want your neck to be wider than the nut, so assuming you don't modify the nut, this will be the distance from the centers of the outer strings to the outer edges of the fingerboard.
To begin my designs, I start with the nut in my cheapo CAD program.
The lines just inside the outer box represent the "E-to-E" spacing given by graphtech on their site. In the case of this nut, it is 1-7/32".
Then I draw a line perpendicular to the nut. In this example, I'm using a 34" scale with 19mm string spacing at the bridge.
Then I draw a 57mm (19mm * 3) long line representing on-center string spacing at the bridge, at the bottom of the 34" scale line, parallel to the nut and perpendicular to the scale line. This is the witness line. It looks like this:
Then I draw a line connecting the outer string notches on the nut to the ends of the witness line drawn at the bottom. These lines represent the E and G strings on this 4-string bass.
From there it's a very simple process of copying and pasting the string lines, and attaching them to the outer corners of the nut.
To complete the fingerboard design, I multiply the scale length (34") by 0.75 to get the position of the 24th fret. That gives me 25.5". To that, I add 0.25" so that there is enough space after the last fret for the end of the fingerboard, giving me 25.75". I then add a line parallel to the witness point exactly 25.75" from the nut, giving me the end of the fingerboard. Last, I delete the string lines and trim the line representing the end of the fretboard to be the exact width of the fretboard, and the core of the design is complete.
From there, I continue with the design for the rest of the bass, adding curves and lines and spaces for hardware.
One of the nice things about this software is that I can get dimensions on just about anything very easily. All I have to do is draw a line connecting 2 points, and the software tells me exactly how long it is. I can also specify particular dimensions for any given line. For example, to create the 34" scale line, I drew a short line at 270 degrees (down), then clicked the length box and entered 34"
, and it adjusted for me.