Breaking in a motor is mostly for brushed motors. You want the connection between the comm. and the brushes seated. Some ways to do it are:
Run your motor in your ride very slow for the first time. This will help get it all seated. I'm not really sure how long to do it, but I would think that one battery pack should do it.
Another way to do it is the water method. You want to connect two D batteries to the motor and run it in a cup of water. After 15 minutes you want to flip the connection so the motor goes in reverse. Don't forget to change the water since it will be full of debris. IMO I like the water method better, but you have to be quick to clean out everything inside the motor or it will rust.