The Navigation screen is where the player plots navroutes. By default, it opens to the in-sector navigation screen, as shown below:
This screen shows a grid of all of the sectors in the current system. To plot a course, simply click on a sector. To plot a multi-leg course, hold shift while clicking on the sectors you wish to plot to. When you hover over a sector, any available information about the sector will be displayed in the pane on the right side of the screen. If you wish to plot a course to a different system, you should press the "Zoom to Universe" button. That will display the following screen:
To plot a inter-system course, simply click on your destination system and click the "Zoom to System" button. That will allow you to plot the course as you normally would.