Flushing the heater matrix involves removing the two heater (supply and return) hoses/pipes - black rubber about 25mm diameter, usually on the passenger side, engine side of the firewall. With both disconnected, insert hose and flush till the other side pipe/outlet runs clear. Reverse and repeat. Basically, you're flushing water not through the engine, but through the heater matrix built into the dashboard.
Does the header tank bubble with the engine running? Does it lose coolant when it overheats?