[surly]

It should not make a difference whether you are writing your program for autonomous or teleop mode, in both cases you should be accessing your motors in the same way because its the same robot with the same wiring.

I think the best practice is to put both left motors on one controller and both right motors on the other controller. This way you can write to each set of motors as a single unit. Having only two writes to the motor controllers will be twice as fast as having four individual calls.

If you are using labview you can re-size the port constant that displays the name of your motor so that in can represent both motors on the controller.