I've looked around the web to get an understanding the setup of the Ardupilot flight modes with a Spektrum DX6 2nd generation and there was none. So I decided to write this blog. The few things to consider when doing this:

1. Please follow the instruction given on the ardupilot webpage.
2. Have the Pixhawk hardware connected to Mission Planner (I have MP 1.3.50 - Copter V3.5.3) 
3. Use the display bar in the Radio Calibration page as a guide while changing the rate pulse widths on your transmitter.
4. I've used switch D to change the pulse width ranges on channel 5.