Running the motor in gear while you brake puts strain on the motor, which would be a last effort to force the air from the system. Just run the car without the rad cap on with the heat on full blast, make sure the thermostat opens and keep the fluid full. Watch and make sure your fans run once you get to higher temps, and that your not getting anymore air bubbles from the system. Some cars have bleeders as well, but not sure if your car does. Anywho if you keep getting constant bubbling usually very "violent" then you have exhaust getting into your coolant system via bad head gasket. Not always the case but a good way to tell, among the typical coolant in the oil, or burning of coolant.
Good luck bud.
