HTML templates are used to define the topic layout of all Help & Manual's HTML-based output formats (HTML Help, WebHelp, Windows Exe and ePub eBooks and Visual Studio Help). What you enter in the editor defines the content of your topics, the templates define the framework in which your content is presented. The HTML templates are stored together with your project.
In addition to this there is an additional set of HTML templates for the special components of WebHelp output (TOC, Index, Search, frameset).
If you are publishing with a skin you must edit the templates in the skin, not in your project! Skins always replace all the HTML templates in your project. Changes made in HTML templates your project will not be reflected in your output when you use skins!
Using HTML templates
HTML templates (Reference)
Help Windows (Reference)