The hot is coming out of the thermostat. The fitting by the water pump is pulling "cooled" water from the radiator and heater core (if it's connected that way). IMHO it really makes no difference which heater hose you connect where as long as the shut off is on the push side (the thermostat housing). I have mine plumbed the way you describe, upper to upper and lower to lower just for the sake of simplicity.

Save a life, adopt a senior shelter pet.
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Name your dog Naked so you can walk Naked in the park.