So I have been given some new default configuration data to stick into GeoServer and I have done so.. a set of six shape files added to the UserBasic configuration. I have left the shapefiles as I have given them, all in one directory, with the feature type's xml files in their own directory as GeoServer has generated them.
Also note that the catalog.xml and services.xml that it uses now (that GeoServer generated for me) are quite ugly.
Richard