I dunno about question 1, but 2 is an easy one. Here is what I did on my bass:
1. Set the saddles to the middle of the adjustment range.
2. Determine what the the scale length is (if you are buying a neck, you must use the scale of the neck, however if you are making your own neck, you can make it to whatever scale you wish).
3. Once the neck is in place, either by gluing, bolting, etc, measure, from the nut, the scale length of the neck. I.E., if you are building a 34" scale bass, measure down the center of the neck 34" and mark the body at that point.
4. Line up the bridge with the marking you just made.
Since your saddles are in their center position, this will give you room to both shorten and lengthen the string to set intonation.
Hope that helps. If I hadn't just woken up, I'm sure I could have given better instructions.