If you want to be able to add a content of a custom content type to a content of Document content type, you've just to add the name of Document content type ('Document') to the CustomContentType.type_info.addable_to attribute (http://kotti.readthedocs.io/en/latest/first_steps/tut-2.html).
from kotti.resources import Document
Document.type_info.addable_to.append('CustomContentType')