In previous iterations of this type of hybrid, you would need to use PX4 firmware (rather than Ardupilot or APM) with heavy customization. Luckily, the newer Ardupilot firmware versions allow for exactly this type of VTOL (they call it a Quadplane). Obviously, the channels are going to be a little different.
The following diagram shows how all of the motors/servos are hooked up:
An easy way to remember motor rotational directions is that the leading edge of the propellers always turn in toward the hull on a Quadplane. Nevertheless, we marked each motor direction (CW for clockwise and CCW for counter-clockwise).
With all of the quad parts on the plane, make sure that none of the quad motors have power, and connections to Pixhawk are severed. You'll want to test-fly (and probably retune) the airplane with the new parts before attempting to use the quad functionality. Make sure you have a successful tuning with the most stable flight possible...