The Mag and Mag Base are just visual representations of the deforming force the magnet causes. The Zone is all that needs to encompass the area, the position of the Base is important though, particularly if you plan on rotating the Magnet. The Mag Base will determine the center of rotation. Likewise, it also determines the center of all forces performed by the magnet. 
For example, if you position the base at the back of a head, and scale in z, the front of the head will be pushed forward to a greater degree where as the back of the head will remain more or less in it's same position. If you position the base in the center of the head, the scaling will be more uniform in all directions.

Hey! His nose is dry! ... Someone should lick it,  just in case. - Diego