Okay let me take a step back. I haven't implemented the PID at all yet. That is purely conceptual and it is where I am going to go with the project once I get the motors spinning at whatever speed I want them to first. Once I get that done, I will be able to move on effectively to implementing the PID on this system. I am using encoders to measure the position of each motor.
I am recreating this machine that I saw from scratch:
