Ardupilot V2.5.1 vs. PiZero

Hello
I have a PiZero and an ArduPilot and I want to know if I can use each components on separate projects or do I have to use both of them together? As you can probably tell I'm a noob to drone building and I'm trying to create my own intelligent Drone with a RoboCat Frame and Cover. Can Somebody Please explain to me the difference between these two components and some best practices for building this drone?  

P.S. I'm trying to build a submarine drone as well 


Cheers!