Take a look at the cross-section image on this page:
http://en.wikipedia.org/wiki/BioSand_Filter

The outlet comes out the bottom and then up to a level that is above the sand. When water stops flowing in the top, the filter doesn't drain completely, only to the level of the outlet.

That being said, I understand that they like best to have a continuous flow. It also takes some period of time with water flowing through it for a brand new filter to develop the layer of bacteria.