Hi @rovedo, welcome to the forum 
For the base setup:
- we have Arduino libraries available for our sensors
- you could use servo control to control the thrusters (although note cross-compatibility issues like this one)
- you could use serial for communication between the Arduino and the Raspberry Pi
I’m not aware of pre-made ROV control software outside of ArduSub, but I also haven’t looked. You may need to write something yourself (basic control could be very simple, but more advanced control can be quite challenging), or you may be able to find something online.
Note that pre-made flight controller boards (like Pixhawks) also include multiple sensors internally. Of particular relevance is an IMU (inertial measurement unit - including one or more of each of an accelerometer, gyroscope, and magnetometer), which helps with navigation and control by indicating vehicle orientation, and estimates of the velocity.