The layout of PDF files and printed manuals is defined in template files with the extension .mnl that are referred to as "print manual templates". These templates are edited with a program called the Print Manual Designer, which is included with Help+Manual.
You can create multiple print manual templates and use them to change the formatting and layout of your PDF files in seconds. this is similar to the skins available for HTML-based output formats.
See Using PDF templates for more details.
In addition to the layout (margins etc), your print manual templates can also add a number of additional optional pages to your PDF documents that normal help files do not contain. These can include front and back cover pages, a print-style table of contents, a foreword, "intro" pages for your top-level chapters, pages of notes at the beginning or end of the document and so on.
You can also create your own addition pages in your templates, insert "snippet" objects that load text from external files or from topics in your Help+Manual project and create multi-column layouts.
In addition to this, PDF documents have layout components that you do not need in electronic help: Headers and footers with page and section numbers, margin settings, formatted headings in the TOC and above topics and so on.
All these features are created and edited in your print manual templates which you can edit with the Print Manual Designer.