What Chris and Bryan said, but let me add that the neck geometry is the most important decision you will make in your design. Melvyn Hiscock has a pretty good chapter about it and it is the one thing that I futz with during the entire time I'm building a guitar.
First simple statement is that the neck to body joint has almost no affect on the geometry. It does affect a lot of other things - access to upper frets, strength of the joint you will be using, the whole way a guitar hangs on a strap. It has a minor affect on geometry in that at roughly the joint (actually more into the heel) the truss rod stops having any affect and there may be some transitions from relief to the fretboard extension. This is highly oversimplified but that little bump or hump or ski jump can cause all sorts of problems
My rule of thumb is that if the fret plane on my guitar just hits the top of the saddles at their lowest adjustable position I always get playable action and have enough adjustment to raise and lower the action as the guitar ages (or my playing style changes). That is a hold over from my acoustic building - I always want a straightedge on the frets to just hit the top of the bridge.
If you would like I can go thru the math but I always make a point of having the bridge I'm going to use in hand when I lay out the neck geometry.
Don't forget that there are two parts of neck geometry - the angle of the neck relative to the top and the amount that it stands proud of the top ("over stand"). The amount that the top is arched enters the picture. The scale length locates where the bridge is on the top but really doesn't factor into the calculations. I always assume that the saddle radius will match the fretboard so that can be taken out of the calcs too.
I'll give you an example - I recently fit a Kahler style bridge to a Jagstang style guitar. The Kahler wants to see the fretboard plane 1/2 inch off the top. The standard Jagstang bridge wants that to be 5/8 and the Warmoth body I had was routed that way. It took a half degree of shimming at the neck pocket to make the angle correct. For what it is worth the scale length is a short 24 inch and the body joint is at the 16th fret - those didn't matter. I routed for the bridge, put it all together and the setup is perfect.