I managed to get the Hexacopter to fly after a few flips on takeoff. It turns out that the motor configuration and wiring for a Pixhawk is not intuitive or well documented.
- You have to search through DIYdrones forums to find the information here.
- Connect motors 1 to 4 to Pixhawk inputs 1 to 4, same as a quadcopter.
- Connect motor 7 to Pixhawk input 5
- Connect motor 8 to input 6