this question pops up from time to time. One thing you have to ask yourself is what neck angle do you want to use. I am a Martin guy and like to build in that style. Martin specs are strings to be 1/2 inch off the top at the front of the bridge.
http://bluescreekguitars.com/blog/ this link will show you how I attain that with consistency . I want to use a 3/8 bridge with a 1/8 exposed saddle. I will go as high as .410 and .150 in the saddle . I try and hold the spec so that I don't get too much saddle height. I can adjust the bridge easy enough on the set up. I use a 1 1/2 degree neck angle. If you use a 2 degree angle you will have to do more adjusting on neck set or go with a higher bridge.
You have to be careful as you ge higher on the bridge you will place more rotational force on the top. When I get the body built I like to pr set the neck so that without a fretboard I will be about 1/16 to 1/8 of an inch off the top at the saddle position. Then when I am finished with the lacquer I can then set the neck without too much work. The variables that you have to look at are , the fretboard thickness , neck angle and fret height. Plot all this into the equation.
This is why I like to have the body pretty far along the line when I get ready to pre set the neck. If I can get it close and only have the finish difference to contend with when I do the final neck set I can dial in the above target number. I can tweak the fretboard thickness and bridge thickness so that the saddle will be where I need it. You can let the saddle a tad higher because in the first few weeks , the top will rise a bit and things move as the guitar takes the load. It isn't an iron clad rule but it isn't uncommon to have to drop things a 1/32 after a few weeks. The neck will take on relief so plan and be aware that this usually happens.
Don't brace tops and brace in high humidity as that can make the top very iffy as winter comes around. Lets see what eles people can add to this
john