What reference point(s) to astronauts use to navigate in space?
Space navigation depends on where you are going.
Most space missions these days are in low Earth orbit. All that is necessary is to know the position of the spacecraft. NASA has detectors designed to do this.
When sending a spacecraft to other planets, comets or moons it is necessary to have accurate ephemerides so that the location of the object is well known. NASA JPL has this information.
For journeys beyond the solar system then the positions of fixed objects such as pulsars and quasars are used.