There are two categories of HTML templates: The HTML topic page templates that define your topic pages in all HTML-based output formats and an additional group of HTML templates used to define the additional components of WebHelp output, which are also used for EWriter eBooks.
Nowadays you will almost always choose an HTML skin to publish your project to WebHelp or HTML Help/CHM. A skin is a special kind of Help+Manual project without topics that only stores your HTML templates and all the settings relevant for HTML output to these two formats. When you choose a skin, the templates and settings in the skin completely replace those in your project.
Normally, a skin is pre-designed and you don't need to change anything. However, if you do want to change something, you must do all your editing in the .hmskin skin file. Editing in your Help+Manual project won't have any effect because those templates and settings are not used.
To edit a skin, make a copy of the .hmskin skin file in your project folder and then open it in Help+Manual by selecting .hmskin as the file type to open in the Open dialog. All the templates and settings are in the same places as in a normal Help+Manual project.
Exception: HTML Export Options
The HTML Export Options section is not stored in skins and needs to be edited in your project.
These are the templates for your topics and they are used for all HTML-based output formats. They define everything in your topic pages except the topic content. They are stored in Configuration > HTML Page Templates.
In addition to this there are also separate templates for the main index.html page and the Table of Contents, Keyword Index and Full-text Search pages used in WebHelp to emulate the HTML Help viewer user interface. These templates are stored in Configuration > Publishing Options > WebHelp.
The WebHelp Layout template contents depend on the layout option chosen
The "No Frames" option disables the Layout template
The layout template is not used at all if you choose the "No Frames" option. Then the Table of Contents template is set as the main index.html file and the contents of the layout template are irrelevant for your output because the template is not present.
HTML Topic Page templates are (almost) always used.
The topic page templates in Configuration > HTML Page Templates are used by almost all HTML-based output formats (CHM, WebHelp, EWriter eBooks and Visual Studio Help 2008 and 2010).
Exception: ePUB and Kindle/Mobi
The WebHelp Table of Contents, Index and Search templates
The contents of the WebHelp Table of Contents, Index and Search templates define three separate pages for these functions. They are loaded into the navigation frame in WebHelp and EWriter eBooks when they are displayed. Some skins load them in the background so that they are always present and can be switched to without reloading.
Templates in the "No Frames" Layout Option
If you choose the "No Frames" option, the Layout template is disabled and is not used. Instead, the TOC template is used as the main index.html file.