When adding modules like: ceon cc, minimum order, dual pricing etc. should I put all the necessary new files into /MyCustom folder??

like these :
includes/extra_configures/minorderamount.php
includes/modules/minorderamount.php

should they go to:
includes/extra_configures/MyCustom/minorderamount.php
includes/modules/MyCustom/minorderamount.php

and like
admin/attributes_controller.php
admin/customers.php

into
admin/MyCustom/attributes_controller.php
admin/MyCustom/customers.php

If yes, are they suppose to overwrite the same file names of original zencart??