The heater valve should be a 2 position 4 way (vacuum operated). It bypasses when the flow to the heater core is shut off.
On the later models with the heated intake manifold, a heater hose goes from the port on the thermostat housing over to the front port on the intake. From the rear port on the intake, a hose goes across and hooks up to the 4-way heater control valve. Yup, 4-way! Both sides of the heater core attach to this heater valve, which allows coolant to continue to flow through the intake manifold even if the heater valve is closed to keep coolant from the heater core. Of course this valve is vacuum operated. The larger (3/4") hose comes out of the heater core, attaches to this heater valve, then continues from the other side down to the port on the water pump.
Hope this helps.
So the manifold and heater core are in series, and the valve basically bypasses the heater core. Makes good sense, as does the vacuum operated.
If I get a chance I'll see if I can locate a Jeep product at U-Pull-It and see if a vacuum dash control will retrofit to the Hornet mechanical cable dash lever. Worst case is the parallel hose system with "Y"s and put up with somewhat less heat (not so bad in So. Cal.).
Right now that aluminum manifold is running dry, and picks up a lot of heat. I'd simply run the water through it with no heater for now but it's 3/4" vs. 1/2" but if its gonna take a while to get allth e parts together I'll make up adapters with copper plumbing.