One of the only disadvantages of raising a SF bed up off the ground is that after a crop is done, the roots need to be removed from the box. This is easily accomplished. Using a hand trowel, simply start at one end of the box and start turning the soil over and removing any heavy roots.
After the heavy roots have been removed, and the soil turned, you can add whatever you feel you need for the next planting. I usually add worm castings along with more compost and rock dust. If your box is on the ground with no solid bottom, this procedure is not necessary.