This depends on how you want your shutters to look. Some folks like thier shutters one way, while others prefer another. There is no real right or wrong - it's simply a matter of taste.
Style #1
For this style, the height of the shutters is about 1/4" less than the distance from the top sash to the bottom sash (A). The width is about 1/4" less than half the width of the distance from the left sash to the right sash (B).
Style #2
In this case, for the height you measure from the top of the bottom sash to the top of the trim (C). Subtract 1 inch and that is your shutter height. For width, measure from the outside edges of the trim pieces (D), then divide by 2 and subtract 1.