The only problem with flushing the whole cooling system is that the heater core has the smallest passages and therefore will clog up with all the crap your flush has loosened. Depending on what is causing the problem, you could remove the heater core and join the hoses going to it with a piece of copper tubing, then flush the system with a caustic and drain/flush again, drain. Clean the heatercore with an acid, I like CLR(calcium, lime and rust remover), then reinstall everything.
Before you do all this, get the engine up to temp and turn on the heater, feel the hoses going to it and they, at least one, should be hot. If not, the thermostat or the heater valve, as mentioned, may be the culprit.
GL
Ed