Filling cooling system. How to properly fill the system? Is it draining into the engine?

The cooling fan is out in my sisters car. She needs a new thermostat and gasket however we continually pour water into the engine coolant and it drains out but not outside the car, it drains into a line somewhere not exactly sure what to do. The car makes a gurgling noise like the car is drinking the water and no sooner we put the water in the car then the coolant pans empty. I don't want her car to overheat or blowup on her. This morning she went less than a mile from the house and shut the car off for no more than 2 minutes and the car wouldn't start even after she received a jump. Can u help us with this problem?