The default layout is to have three frames:
This frame shows a tree heirarchy of the modules or files in the project. Clicking on a link opens that module or file in the "index" frame below.
This frame shows an index of the currently selected module or file, but only shows child classes, structs, namespaces or modules. When a module page is loaded in this frame and you have JavaScript enabled, a more detailed page will open in the main content area. For file pages you will need to click the "File Details" link.
This frame shows the main documentation. At the top of each page you can see a list of documentation areas you can visit: The Modules and Files open in the top-left frame, the Inheritance Graph/Tree and Name Index load in the main frame. For "scope pages" (i.e. the pages for classes and namespaces, including the global namespace which is the default page) the page is divided into summary and detail sections: the summary shows all the declarations in this class or namespace, with a summary for each. For declarations with more comments than just the summary, the name of the declaration will be highlighted, and clicking on it will take you to its detailed information further down the page.
This three-frame layout is inspired by JavaDoc, which is similar, but turns out to be less useful than it might be since most projects don't have a nice list of packages to go in the top-left frame like the Java libraries do. You will notice from the Synopsis RefManual however that an extensive Python project can fill the frame quite well.
To enable the three-frame layout, the FramesIndex page must be included as the first Page. You should also have at least one of ModuleListing and FileListing, and ModuleIndexer and FileIndexer to fill in the frames.
If you don't want frames then don't include the FramesIndex page. Whatever Page comes first will get to have the "index.html" page. For example, if ScopePages is first, then the index.html page will be the Global Namespace page. If DirBrowse is first, then it will be the listing of the project directory.