A major help to organize your contents is to think about your
content in terms of "publications". A publication is a container
of (HTML-) objects with certain properties. A good way to implement
a publication is to create a subdirectory with a "index.html".
Within this directory, you can put other files related to your
subject.
For each specific subject create a new directory and put an
"index.html" into this directory, serving as a "homepage" for
this subject. This way, you can better group files that belong
together. Finally, SiteC references your new directory in the
navigation bar and thus allows to navigate straight to your contents
(just replace the bare directory name in the navigation bar by
a short title).
The link checker recognizes links to directories if a file
"index.html" resides inside the directory.