everyone has a different thought to this. my guy told me to go out and drive around for a while. let them cool. go out and drive some more. let them cool down. (repeat a few times) and then go out and drive the hell out of it.
i had no gear whine when i had the 4.10:1 ring and pinion set put in with a new frpp t-lok differential. i got the car in the afternoon, drove 30 minutes on the highway to the track, ran 4 passes, and everything is perfect 14 months later... if they are set up properly, they should not whine and you should not have to worry about "breaking them in"