The shut-down solenoid, which is on top of the pump, requires 12 volts to stay open. So if you want the engine to run, you need to give it 12 volts; otherwise fuel won't get to the injectors.
The other wire goes to the KSB, which advances timing when it's cold out. Whether or not you want to give that voltage depends on whether or not you want to use it to advance the timing, and also depends on if it's an early-model long-and-skinny KSB or a later-model short-and-stout KSB.
The early ones advance timing when they have no voltage, the later ones advance timing when they do have voltage. The date they changed was 91.5, so you should have a later model.