The layout template is the "frameset" template that defines the frames containing the topic pane and the navigation pane, and also the header frame if you are using a three-frame layout. Basically it only provides the external framework and tells the browser which files to load into which frames. This means that you should not normally have any reason to edit it.
This template is highly specialized and should only be edited if you have advanced HTML editing skills. It is essential for the proper functioning of the entire navigation system in Webhelp and editing errors you make here can easily make your help unusable.
See Editing HTML templates for details on how to edit templates.
Template location
Configuration > Publishing Options > Webhelp > Layout
See also:
HTML template output conditions
Page url: http://www.helpandmanual.com/help/index.html?hm_advanced_htmltemplates_layout.htm