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).
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.
Using HTML templates
HTML templates (Reference)
Help Windows (Reference)