If you're not using the current-sense feedback circuitry, by far the easiest place to "tap into" the Arduino with the motor shield attached is on the 2x9 header shown below. You could, for instance, pop off the jumpers and use female DuPont style cables. Actually even if you are using the current-sense feedback, on the 4-way Motor Shield, A4 and A5 are up for grabs.
The pin I've marked with a red dot is 5V, the pin marked with a blue dot is GND, and the orange dots are A0 through A5 respectively. As you may already know, the Analog Inputs on the Arduino are perfectly fine to use as Digital GPIO as well (technically they are D14 through D19 when used that way).
Also, if you haven't already come across it, the User's Guide and other resources on this page can be quite helpful in getting oriented to the capabilities of the board.