The cabin heating and motor cooling circuits meet and mix in a tank that'll be installed under the car. From here, a new pump will pump coolant to the heater core (the pump that currently does this will be used to pump coolant through the electric heater only). Yes, both circuits use the same coolant.
The way I have this designed, the car has no knowledge that the two circuits would now be one. The HVAC system would function just as it does now (so it doesn't interfere with QC cooling). I would install a switch to detect the position of the heater damper, which either directs air through the heater core or bypasses it. The system would only pump coolant through the heater core when both the cabin fan is on and this damper is directing air through the heater core.
So, to use recovered heat to warm the cabin, simply turning the fan on and leaving the temperature knob on the green dot should be sufficient. If there isn't enough heat in the coolant loop (or you want a boost), you simply turn the temperature knob up into the red to activate the electric heater and the HR (heat recovery) system will automatically separate the heating and cooling circuits while the electric heater is on, making it function just as the car does from the factory. When you want to switch back to recovered heat, leave the fan on and turn the temperature knob back down to the green dot (being careful not to accidentally click into the Blue portion. If you do, simply turn back into red, then to the green dot). The circuits will stay separate until the mixing tank falls back to the temperature of the coolant loop, and at that point, the two circuits will become one again.
The only caveat I'm aware of right now is that the front reservoir can't be used, as using two vented tanks would result in losing coolant. The coolant reservoir in the back of the car is vented, so the one that will be installed under the car must be ventless and must be below the vented tank (which being under the car, it would be).