Make sure that your Arduino is connected to your computer via USB.
From the main menu, choose Run -> External Tools -> External Tools Configurations....
Select Program.
Press the New button to create a new configuration.
Set the Name to Write Flash.
Set the Location to the full path to AVRDUDE.
Set the Working Directory to ${workspace_loc:/${project_name}/Debug}.
Set the Arguments to: -c arduino -p atmega328p -U flash:w:${project_name}.hex:i -P /dev/ttyACM0
You will need to make sure the serial port (-P) value matchs the the port of your Arduino.
Press Apply.
Press Run and AVRDUDE will write the HEX file to your Arduino.
If all goes well you should see output simlar to this in the Console view: