That is addressed in the FAQ:
Which pins are connected to the DC/Stepper motors?
The DC/Stepper motors are NOT connected to the Arduino directly. They are connected to the 74HC595 latch which is spoken to by the Arduino. You CANNOT talk directly to the motors, you MUST use the motor shield library.
To control the motors you need to control the H-bridges via the 74HC595 latch. The latch is controlled by pins 4, 7, 8 & 12.
Source code for the library and full schematics can be downloaded here: http://learn.adafruit.com/adafruit-motor-shield/downloads