When I set up a dovetail jig (1/2" fingers), I scribe a mark 1/2" on the left edge of the top (pin/end) board. That's the offset for the side (tail) board. Using this as an alignment mark you don't even need the side stops. You can cut the boards in the middle of the jig. However, most people would rather use the parts they paid for and want the side stops to perform their function. Setting the 2 boards to this mark should help you get the side stops in their proper places.