The layout of Help+Manual's PDF and print manual output is controlled by template files called "print manual templates" with the extension .mnl that do much more than just define the appearance of your pages. These templates can also add front and back covers, multiple title pages at the beginning, an introduction, a formatted table of contents, title pages for individual chapters, graphics, headers and footers, a formatted index and multiple endnotes pages. You can also define your own additional pages and insert topics from your project or external files with a "snippets" function.
All the global variables and user-defined variables from your project file can be used in your print manual templates. Since the templates are external files you can use them in multiple projects, applying them to your output just as you apply skins to HTML-based output formats.