The mission planning software is available at http://planner.ardupilot.com/. There are actually two applications available that perform similar actions, but the Mission Planner is a good place to get familiar with how to talk with your quadcopter from a computer program.

To do this, you'll need to make sure that you have telemetry radios connected to the Pixhawk and the computer. This will prevent the need to directly connect to the Pixhawk with a long USB cable. When you begin the mission planning software, you will see the following screen:

This is the basic screen. You'll then need to configure your radio's COM port and then press the CONNECT button in the corner on the upper right-hand side of the screen. As you move the quadcopter around, you will see the measurements change. If you are having problems connecting to the Pixhawk, there is lot of help available on the website.

Now that you have connected, you can actually see how your quadcopter is flying with this...