I'm afraid that your explanation is not clearly phrased, but I will try to assist you with some general advice. It would help if you were to provide a link to the website in question.
First of all, the list of available main menu entries is at /admin/structure/menu/manage/main-menu: there, you can disable any of the defaults or add your own. Book page menu settings are handled the same as those of any other content type, so go to /admin/structure/types/manage/book and select the Menu settings tab: there, you can dictate which menus are allowed to show book pages.
To adjust access to particular book sub-pages and/or their parents, choose the applicable page from /admin/content and you will find that it, too, has a Menu settings tab. This allows you to decide whether it should have a menu link somewhere and what its parent should be. For example, my site is configured to show two book parents in the main menu and one in the navigation menu, but sub-pages are not in any of those menus (they are just shown on their parents).
Note the next tab below Menu settings, which manages a few simple book outline settings for each book parent and sub-page.
Currently, a link to each page is shown at the bottom of the page.
That is an example of what I meant about clarity. In case it heps, book sub-pages are expected to contain links to the previous and next sub-pages (when applicable) in the same book and the parent will show a link to the first sub-page. These appear below the content. Additional (though less flexible) control can be had by altering your theme's book templates.
I recommend that you experiment with major and/or complex changes on your test installation before getting too far with alterations to a live website. Drupal's IA (information architecture) is flexible and quite sophisticated, but as with all IA, it can benefit from some planning ahead.