Using a TIP122 to control a motor
Wire the Arduino PWM pin to the Base of the TIP122 through a 1kOhm, or at least 270 Ohm, resistor in series. 
Wire the TIP122 Emitter to Ground of the Arduino.
Wire one lead of the motor to the positive side  of your battery pack, the other lead to the Collector of the TIP122
Put a diode across the leads of the motor, perhaps a 1N4007, wired reverse biased (cathode towards battery positive in previous point).
Add an electrolytic capacitor of say 10 uF 12 Volts in parallel with the diode, connected with its negative lead (usually marked) towards the Collector of the TIP122
Wire the negative of the battery pack to the Arduino ground.


This article has a description and a schematic: Scroll down to the section titled "DARLINGTON TRANSISTORS AND HIGH CURRENT DC DEVICES"