One runs from the water pump, the other runs to the coolant port on the front passengers side of the intake. The rear ports are meant for cross over cooling front to back often used on race cars and not needed on the street.
As for inlet and outlet that's easy, the size of the heater core outlets will tell you which is which as one is 5/8 and the other is 3/4.
3/4 goes to the water pump. 5/8 goes to the intake.