You break in your subs by playing them at low levels. You do this for a week or two depending on how much you listen to them. If you don't do this then just take your subs outside and shoot them with a shoot gun. Either way you can damage the voice coils. I have also seen the surrounds come apart on subs from not letting them break in. I always let my subs break in for about 100 hours. Doing this I have never had a problem with them.
play the speakers at low to moderate volume for the first 20 hours or so. this gives time for teh spider, surrounds, etc to break in and loosen up. you'll notice as they break in tehy will start to sound a lot better. cranking them up right out of the box can shorten their life, and won't give you optimal performance.
I've always hooked mine up to my pro audio amp (Mackie 1400i) and fed them pink noise at a moderate level for about 24 hours... or is this just another 'controlled' way for those who don't have the patience when they're installed in their car?