"The black wire (negative) must be connect to the same negative rail as the Raspberry Pi."
I said that, because you can run the motors from a separate power supply from the Pi, but they need to be referenced to the same "ground" level.
Two batteries which are not connected in any way, are just "floating" relative to each other with no particular voltage between them, and circuits can't interact (unless you use a special component such as an opto-coupler or relay) as they don't have a common reference voltage. There is no return path even for the small amount of current needed to send signals.
In most cases, this means you need to connect the GND or negative terminals together somewhere in the circuit - it really doesn't matter where, because hopefully very little current will flow back through this path.
If, for example, you put two power banks in your robot, and use one to drive the pi and the other for the motors, it won't work unless the negative is connected together.
Also, yes, pootle is correct, you need to run the pigpiod process.