This is how I do it.
Assuming you either have the actual neck in your possession, or a good CAD model of it, start with the location of the nut, and work your way backwards. That is, if you already have the neck, then you know the scale length. Scale lengths are typically 25.5" for Fender-esque guitars, and 24.75" for Gibson-esque. (You can't use a 25.5 neck for a 24.75 scale length.) If you're going to make your own neck, you can make the scale length whatever you choose.
The position of the neck, and the nut, determines where the bridge needs to go. You can adjust the location of them (as a set) to suit your design intent.
A good rule of thumb is (assuming your going to use a 25.5" scale length), it should be 25.5" from the nut to the skinny E string's saddle, and then about another 1/8th inch for each successive string, due to intonation allowances. Not exactly, but a good rule of thumb.
BTW, what CAD package are you using. Nice design!
Hope this helps.
Jeff (aka Johnny501)