I have my arduino Uno giving commands to a motor controller. The motor controller is taking 12V externally, and has a regulated 5V output available. What pin do I connect the 5V output to on the arduino to power it as well?
To power ur arduino you can connect 5v output to Vin pin of arduino right next to the A0 pin . But its better you give a separate supply for arduino and motor controller.
It is not a good idea to use 5V pin on the arduino to power the board as it does not go through the voltage regulator. The best option is to make use of the Vin pin. This one goes through the regulator. Then when it comes to the motor, you will need to have a separate supply. But make sure that the grounds of both the supplies are connected. The best thing to do is to use a single 12V to drive the motor and also power Arduino. But make sure that you connect 12V supply to the Vin pin or through the plugging jack provided.
All the best
It is also worth noting that if you give the Arduino 5V on the Vin pin or via the barrel jack the voltage regulator will not be able to make 5V as it needs to drop some voltage to do so. This will result in your 5V pins running significantly short of 5V. You may be able to get away with that in some circumstances, as the ATMEGA 328 chip is quite forgiving, but you really should avoid it.
If you have a 5V supply that you are willing to place your Arduino's life in the hands of, then you should connect it directly to the 5V pin or through the USB connector. Such a power supply should at the very least be capable of supplying the current you need, have some capacitive filtering, and be relatively immune to high voltage spikes and noise. I would tend not the use the 5V supply from a motor driver because motor drivers tend to generate a lot of noise due to the high currents they control, and I would rather keep separate from the rest of my circuit. All of this does not mean that it wouldn't work (in most cases it would), but it would be better practice to do something else.