Unless I have the permissions set up wrong, you should see a book tab at the top of each article. Clicking on the tab will open the list of books with radio buttons for each book. Select the one in which you wish to include the article.
You can use BOOK namespace references inside any article or any post on the message board. You cannot put a book inside a book. That structure is only one level deep.
If you use the syntax [book]Name of the book[/book] there will be a reference to the book.
You can do similar things with CATEGORY, but in that case you need to use the format [category = "CategoryName"]Words describing the category[/category]. I believe you can use that format for the book reference also, but I have not studied that.