Dear Gemma,
you indeed want a feff-input with a central Co on/in a kaolinite matrix. You should define the location of the Co ion - the simplest assumptions would be substitution of an Al or Si.
Import the cif and run ATOMS to create the kaolinite structure. Then replace either Al or Si with Co (index 0) in the atom list and change the atom with index 0 to Co with its atomic number. Then run FEFF and do the fitting!
Before running FEFF, control the atoms list and visualise your structure in a molecular program (e.g. Mercury) to make sure that the structure is as you wanted - Artemis sometimes builds the structures incorrectly. To export an atom list in .xyz format, Theory --> FEFF --> write special output --> xyz, save the list as a .xyz text file and open it in e.g. Mercury. If you get errors, try another cif file of kaolinite.
All the best!
Alexey