Regarding the Book navigation, if you need to move the navigation block at the top of the default main content, you should edit your node template. Edit your node.tpl.php template into your theme folder and add the following code:
<div class="content"<?php print $content_attributes; ?>>
<?php print render($content['book_navigation']); ?>
// We hide the comments and links now so that we can render them later.
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