The running in process is to allow for the time taken for certain components (such as capacitors) to settle and perform at a constant. The amplifier will sound good out of the box, and will only improve as it is run in. This running in time can vary, but we generally quote about 36 hours.
You can do this all at once if you want your amplifier to be run in quickly, or you can use your amplifier normally and allow the 36 hours to build up over time. The overall result is the same.