Running it through the heater should not be necessary if the cooling system is set up correctly with no problems. Running the coolant through the heater is usually just a band aid for a faulty cooling system. It usually indicates another problem is there but doing this masks it up.
I am including some cooling system thoughts that may make unserstanding what happens in your cooling system as bit easier.
When building any "Serious"

engine you should hot caustic tank the block and head. This process helps remove scale and oil from the cooling system. Drill all the water gallery holes on the block deck to clean them of any corrossion.
If the head has been serviced correctly and there is no corrosion in the water jackets, you have a fighting chance of survival in a race engine.
The next most important thing is to keep the coolant pressure sufficiently high so steam bubbles do not form around the coolant galleries.
This means that you must run a thermostat and give the coolant enough residence time to absorb as much heat as possible without being able to form steam bubbles.
The following is a simple diagnostic cooling test any one can do at no cost. It is suitable for A series, L series, CA FJ or SR's etc.
On the inlet side for coolant flow back into the block/head, fit the cap end of a 1.25 or 2 litre coke bottle into the hose on the block inlet side. Cut out the base of the coke bottle to make it like a funnel and fit the heater return line into the top of the funnel section. You may have to make an extension hose up to carry these tests out.
Half fill the funnel with water, then holding the bottle up, remove any air from the radiator cap. There should be sufficient water in the funnel so the coolant level remains relatively stable with the engine running. Top the coolant level in the funnel up with additional water to maintain the coolant level in the funnel at a constant level.
Bring the engine to a constant operating temperature. To test water pump pressure raise the coolant delivery hose into the funnel so the coolant from the heater return line falls in an arc into the top of the funnel. At approximately 800 rpm idle, the hose should be able to be raised 450 -600 mm before coolant flow stops. This indicates a coolant pressure of approximately 1 psi. If the flow level falls below 300mm before flow stops, the pump is not providing sufficient pressure for the system and the pump must be replaced.
Next look for pump cavitation by running the engine at 2000 rpm and looking at the changes that happen to the coolant. If it goes opaque or cloudy like the head on a freshly poured beer, you have some cavitation. If the cavitation is bad, large bubbles will appear in the funnel rather like the aerator bubbles in a fish tank.
If you have either symptom you should look at the water pump type you are using and the pump drive speed.
Often by slowing the pump or removing some pump blades or cutting them back, these symptoms will dissapear.
The tests were shown to me by "The Professor" John Bennet of Perfectune Engineering (Yella Terra) fame for those of you old enough to remember.
Hope the info helps.