There are a lot of misconception on the power rail, please look up what it is. Basicaly, all the + pin are bridged together but not connected to anything (this was not exactly the case on mine, so be careful), this way you input the voltage/power you want on the rail, and it will not disturb the flight controller that should use a second power unit for stability reason.
The PWM pins (relative to the ground pins) are the ones that are connected to your Pixhawk.