In this past Robotalk session someone had asked about how to use two encoders for a four-motor drivetrain, and so here I am! I will be using the motors known as "Left Motor 1" and "Left Motor 2" as examples. What I have found works best is if you hardwire Left Motor 1 and Left Motor 2 to the same motor port in the DC Motor controller. If you look at the picture below, you can see that I have soldered both Left Motor 1's and Left Motor 2's negative wires together. I then added a third wire that connects to the DC Motor controller. If you do the same for the positive wires, you will have the robot "think" that it is only controlling one motor when it is actually controlling two. Then simply add an encoder to one of the motors (doesn't matter which one you pick) and then those encoder values will apply to both motors.
Hopefully this helps,
Trevor A. Babb
The Hard-Hitting Hardware Hooligans