Please refer to https://github.com/gmacario/learning-arduino to get the Fritzing schematics and the corresponding the Arduino sketches.

Read documentation at http://arduino.cc/en/Main/ArduinoBoardYun

Start Arduino IDE (version 1.5.6 or later)

Arduino: File > Examples > 01.Basics > Blink

Arduino: Tools > Board > Arduino Yun

Arduino: Tools > Port > COMxx (Arduino Yun)

Arduino: File > Upload

Verify that L13 is blinking every 1000 msec

Adjust the values in the delay(xxx) instruction after each digitalWrite, upload the new sketch and verify that the blinking rate is changing accordingly.