John,
I'm sorry, this does not qualify as a stupid question.
I would think you'd want that first ("zero") fret cut as well. You could later cut it through the rest of the way with a hand fretsaw, but at least you'll know where that mark is.
Same thing with the upper end of the fingerboard. Unless you had some other specific spot where you want to cut it off, I'd use the template to cut the 21st fret for a 20 fret fingerboard, and then later cut through that 21st fret line the rest of the way by hand.
Dennis
