Most DC motor controller boards and shields (like the popular ones based on the L293 and L298) for the Arduino allow you to power the motors via an external power source. Some require the Arduino board to supply the logic supply for the h-bridge; others have an on-board regulator, and can take the power from the motor supply. Some have jumpers to select what you want; some can even power the Arduino (ie, the supply for the motor and driver board also powers the Arduino).
Above all else, you need to know the voltage of your motors, and the worst-case (stall) current needs of them - before you can select -any- controller. If you don't have a multimeter to measure this, that meter should be your -first- purchase.