The preferred method of navigation on anything newer than a "six-pack" is a "Moving Map GPS", that shows the position and course of the aircraft on a map of the environment, including airspaces, airports, waypoints, and major landmarks. Many systems also show terrain, weather, and other air traffic.
Route planning is done by entering the origin, destination, and any waypoints along the way. There are however instances where plain coordinates are used, such as in oceanic flights.
When the GPS is coupled to an Autopilot, the autopilot can fly virtually the entire route other than takeoff and landing. But pilots must always be monitoring to address ATC instructions, weather, traffic or other issues.
GPS can occasionally have disruptions, so most pilots keep paper maps handy, and cockpits have a magnetic compass. Pilots should be prepared to navigate with nothing more than a map, compass and stopwatch if the need arises.