I wouldn't run all my coolant through the heater core.
1 - The heater core connections are much smaller than the rest of the cooling system, so you'd severely limit flow, making it more likely to overheat.
2 - If you turned the heater control to cold then you'd stop all flow through your engine, overheating it.
Run a proper water setup, there are plenty of photos around of how things are setup stock, and how they can be modified. Have a bit of a dig and you will find something you can use.