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Yes, I think that's essentially correct. The arduino code accepts simple single character commands, and replies back over the serial port. The code is not very complicated.
I just did the same thing you're talking about, I created a new motor_driver.cpp and encoder_driver.cpp file. I just wrote my own readEncoder(), resetEncoder(), resetEncoders(), initMotorController(), setMotorSpeed() and setMotorSpeeds() functions.
-Jon