The datafiles directory was introduced in the samples directory during 0.4 iirc. The name 'datafiles' is not mandatory; it is just a container directory of the required cegui xml files and their parser validation files (xsd). For example if you have those directories (schemes,fonts,layouts and such) inside a 'resources' or 'media' directory, that is fine as well.
You can check the CELayoutEditor.INI file for some settings. 'CurrentLayout=' denotes the last openend layout file. Note that it uses resource groups, meaning that it will always try to load your layout from the directory which is set in the 'LayoutsPath=' line. Maybe that is causing your problem if you saved your layout into another path. That is something i still need to look into, because it is confusing.
If you want to know more about resource groups, please read this page:
http://www.cegui.org.uk/wiki/index.php/ ... s_in_0.5.0