All new speakers need to be 'run in' properly before they will sound their best.
This is because the drive units are extremely stiff straight out of the box and require running time to 'free up' a little and move fully as they are intended.
Running in the speakers is simply the time that it takes for these units to loosen up, allowing the speaker to create a smoother and more pleasant sound with the correct amount of bass.
Speakers can be 'run in' in a couple of different ways.
1. Just hook them up to your system and use them normally. This will take a bit longer but you dont have the inconvenience of a few days without a system to listen to. Usually the speakers will be sufficiently run in after a total of 20-30 hours of normal use. They will often continue to develop and improve for the first hundred or so hours of use.
2. As the guides suggest. Run them face to face, millimeters apart, out of phase, playing music constantly for a couple of days. This is the quickest method but means that you dont have a system to enjoy for a few days.
There is no harm at all in running them out of phase - the reason for this is that the overall noise is lower because the phase reversal means that each speaker cancels out much of the other's sound, so you can turn the system up louder to really get the drive units moving and run-in quicker.
Ultimately, its up to you which option you choose - the end result will be the same.
As the drive units are quite stiff/inflexible to begin with, running extremely high volumes through them for the first 10 hours is not advised.