Electronic – arduino – Wiring a switch to toggle both usb power and external power on Arduino

An Arduino Uno can be powered by

• a stable (regulated) 5V DC, which you can either supply via the USB power lines, or via the shield connectors, or
• an unregulated 6-20 V DC (7-12V recommended), which you can supply via the 2.1 mm centre-positive barrel plug connector.

I would not recommend using a 9V battery, because its voltage will drop quickly, but in a pinch this can be used.

ref: http://arduino.cc/en/Main/ArduinoBoardUno

The grounds would generally need to be common.

That said, if the motor side has its own power source it is possible to isolate the PC/Arduino portion of the system from the motor part of the system by connecting all the motor control signals through opto-couplers. This would permit the motor subsystem ground to be separate. Note that really cheap opto-couplers can limit the bandwidth of the signals going to the motors so if you are using high frequency PMW controls make sure to evaluate and select components accordingly.