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In addition to varying the content of your output you will often also want to vary the layout and appearance of different versions of your project when you publish it. How you do this and what options are available depends on the output format you are using.
The HTML templates used in WebHelp and CHM are stored in your project and are fully editable. You can have multiple templates for topics stored in a single project but only one version of the templates for the navigation panes (TOC, Index and Search) used in WebHelp. The multiple topic templates are primarily useful for having different layouts for different topics within the same project.
If you have the Professional or Floating license version of Help+Manual you can save all the templates in your project in a "skin" that you can then apply to other projects to change their layout.
The layout of your PDF output is defined in special layout files called print manual templates, with the extension .mnl. You can edit and create these templates with the Manual Designer program included with Help+Manual, which has extensive help and tutorials of its own.
Like skins for HTML-based formats, PDF print manual templates can be selected in the Publish dialog with a single click. This makes it possible to apply a completely different look and feel and/or corporate branding to a document in seconds. In addition to the general page layout, the PDF template defines the front and back cover pages, the layout of the table of contents, additional pages like the Foreword and end notes and intro pages for top level topics, user-defined pages, headers and footers, page and section numbering styles and so on.
See PDF and Printed Manuals for full details and instructions.
Help+Manual can generate two different kinds of eBooks: Windows EXE eBooks and ePUB eBooks. A number of pre-designed layout templates for EXE eBooks are included. Formatting options in ePUB eBooks are quite limited and alternative templates are not an option because the strictness of the ePUB format means that the templates should not be edited.
Word DOCX is not generally a primary choice as a documentation format. If you want to provide a printable version of your documentation use PDF, if you want to provide an interactive help system use CHM or WebHelp, if you want to provide an eBook use ePUB or Windows EXE eBooks.
Even so, you can configure the layout of your DOCX output in Help+Manual very extensively with special DOCX template files that you can create and edit directly in MS Word. See the MS Word DOCX publishing chapter for details.