you need to re-plumb your entire engine, you need a different thermostat housing in either case
if you are running a half system, the discharge of the HX runs into the manifolds, and then the manifolds are plumbed to the elbows and the water exits. the thermostat is plumbed similar to a car's system here.
if you are running a full system, the discharge of the HX runs to the elbows. a full system uses the thermostat as a mixing valve to regulate temp
however you cant clean the shell side of the heat exchanger, and installing a heat exchanger on a used motor means that you simply use the heat exchanger as a really expensive cooling system filter.