Override for dual pricing, min. order, etc.

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??

Most all modules are packaged as to where the files contained are to be located.

So you need to see the install instructions for each individual module

Should two modules overwrite the same file, what is the proper procedure??

If you have 2 mods that have alterations to the same file first you have to determine if they conflict by setting the same fields/functions differently.

If not, the you must merge the contents into a single file to get both the functions.

Make good notes on this for future upgrades and issues.