The user preferences allow you to customize the behavior of certain options in the help file builder that apply to all projects and the environment in general. The User Preferences option can be found in the standalone GUI on the File menu. In the Visual Studio extension package, only the general options apply and they can be found by opening the Tools | Options dialog and selecting the Sandcastle Help File Builder category.
General Preferences - Standalone GUI and Visual Studio package.
Spell Checking Options - Standalone GUI only. A separate spell checker package is available for Visual Studio. See the page in the guided installer for details.
Content File Editors - Standalone GUI only. The Visual Studio shell handles opening files with an appropriate editor. Custom editors are defined using the Open With context menu item on project files in the Solution Explorer should any be needed.