The water pump with two 'heater' ports is made so that each port just shares the flow. The bottom thermostat housing is the same way sharing the flow with the top thermostat housing. It is customarily connected:
1: Upper T-stat housing to upper waterpump connection #1 2: Lower T-stat housing to heater 3: Heater to waterpump connection #2
I think that is right. Others will say if it's wrong. The Heater Valve you refer to is for closing off the flow/heat during the summer months. It is really a duplicate circuit with the true bypass thermostat housings. You can run two heaters if you choose, or you can run two bypasses.
