Include documents contains one folder if Show details in the View menu is turned off i.e., Included by. The Included by folder contains the documents that include this include document. This will not show which specific revision of this document. To see that the 'Show details' setting must be on.
If Show details in the View menu is turned on include documents contain two folders: Document Revisions and Included by. The Document Revisions folder contains all revisions made of this document. The Included by folder contains all documents with their specific revisions that include this document.
Note that the ITP/MDK Repository tries to resolve an __INC tag by searching it's include paths. If an include document is placed inside an include subfolder this subfolder should be set as an include path in the project or this subfolder needs to be put in the __INC tag as well. A subfolder that is not set as a search path has a slightly dimmed include icon.
Example
MyInclude.doc is placed in the MySubInclude which is a subfolder of MyInclude. MyInclude is set as a search path of the project. In the model document, then, MySubInclude should be placed in the __INC tag: __INC(MySubInclude\MyInclude.doc)