User is the location for your personal customizations. Typically, it is C:\users\(name of user)\Autodesk\Softimage_2012.SAP on Windows or ~/Autodesk/Softimage_2012.SAP on Linux. This is the default location for storing new customizations that you create.
Installation (Factory) is the location for presets and sample customizations that ship with Autodesk Softimage. It is located in the directory where the Softimage program files are installed. It is not recommended that you store your own customizations here.