Classifying something under "Articles" instead of "Topics"

First off, I'm sorry if this has been asked elsewhere. I've found a lot of other threads where I feel similar questions are being asked, I'm just having trouble understanding how everything fits together.

Ok, so by default in the Primary links, there are links to broad classes of articles (Business, Health, Politics, etc) and subclasses (under Business there is Finance, Markets, etc.). What I want to do is add to/change this list of Primary links. So far I have been able to go into /admin/build/menu-customize/primary-links and add different topics that I created in the Taxonomy section. The result is an additional link pointed to site/topics/topic-classification the Primary Links, but I haven't been able to add anything as site/articles/article-classification

What I want is to be able to add to what is classified under site/articles. For example, what if I want there to create an article on the book The Great Gatsby and, under Vocabularies, choose "Fiction" which is nested under "Books".... and then have a "Books" link in the Primary Links with other links like "Fiction", "Non-Fiction", Biography, Reference, etc. nested under it, each pointing to site/articles/fiction, site/articles/non-fiction, site/articles/biography, etc. With this setup, the article on The Great Gatsby would show up on the page site/articles/fiction.

Thanks