All input should be given in atomic units.
Update: While charges should indeed be listed in atomic units, the units for distances depend on the user input. If the structure is specified in Ångstroms (the default), the coordinates for external charges should also be in Ångstroms. If the structure is specified in atomic units, the coordinates for external charges should also be in atomic units. (See INPUT_BOHR.)
$external_charges x-coord1 y-coord1 z-coord1 charge1 x-coord2 y-coord2 z-coord2 charge2 $end