Looks to me like they both function the same due to the pump housing shape, but you have a choice of small or large hose fitting.
The heater has 2 different sizes coming off of it, so the one that doesn't fit the intake fitting would go to the corresponding fitting on the water pump.
That said, it looks to me like you would use the one closest to the crossover just like the old pump did and plug the larger one off.
