If you stop the flow in either hose it will keep the coolant from circulating but there will still be fluid in the heater core. Stopping it on the pump side might slightly reduce the pressure in the heater but unless you have converted to a pressurized cooling system it shouldn't really matter. I added a simple cable operated valve in my truck so I could regulate the flow from the cab.
http://i99.photobucket.com/albums/l286/Hookalatch/Heater/IMG_1752.jpg