Above the lid of the box. It depends upon the height of the bridge and the height of the strings above the neck.
As Duck said there are a few factors, I do like a bit of a gap to the body so my pick isn't always banging/scaping the top.
Somewhere between flat with the top and like a violin. Whatever makes your hands happy.
Set the top of the fretboard around 7-10mm above the top of the box if you are using a floating bridge. If you are using a "hardtail" bridge, the top of the fretboard should be 5-6mm above the top of the box.