Hello people, I am new to ardupilot!
Currently, I just got my pixhawk and I am working on it to build a underwater robot.
I really need a lot help from this! I am trying to use the IMU and PWM pins from PX4 board.
I am using Kinetic ROS to control my thrusters with arduino.
Someone please teach me how to use PX4 with ROS. 
You will need to construct an adapter from usb to serial. Then install mavproxy and mavros. That is about it. You can use the Pixhawk as little or as much as you like.http://wiki.ros.org/mavros
I think you can use the telemetry port as the communication bridge between two systems. please take a look at the tower code. and mavlink for example.
If you’re using a pixhawk, the easiest way would be to use Ardusub which is specifically designed for underwater vehicles.
There is an arudsub!?