Some questions on the Arduino Motor Shield R3

Other Hardware Motors, Mechanics, Power and CNC
3

If you're using a motor shield the motor & arduino connect to that.
Have a look at thesetutorials:

http://udanis.com/arduino-motor-shield-tutorial/
http://playground.arduino.cc/MotorControlShieldV3/0
http://www.tinkerkit.com/arduino-motor-shield/