I think that you have two options.
1. Break it in with the motor saver air filter.
2. Break it in, then reset the needle to factory settings, put the motor saver air filter on, and retune for performance.

I think that either way would be fine but I would go with the second option just because I like seeing the change in performance and it might be a little safer to break it in with the stock air filter so it wouldn't be a variable to the break in and throw the break in off by a bit. Thats just what I think maybe it could throw it off mabe not but I would rather do it right instead and then changing the the air filter.