WebOffice 10 R3 introduces the concept to reuse the ArcMap table of content. Therefore the ArcMap table of content should have exactly the structure, names and visibilities that you would like to see in the WebOffice 10 R3 client.
Anyway it may happen that for specific projects you cannot use exactly the same in the WebOffice 10 R3 client like in ArcMap. Therefore it is possible to override ArcMap table of content definitions by redefining the elements of the Table of content in the WebOffice 10 R3 project configuration again.
Using the WebOffice 10 R3 project Table of content configuration, it is possible to add certain properties to existing elements of the Table of content, e.g. metadata information and properties on map service level which are not represented in the ArcMap table of content at all.
Note: WebOffice 10 R3 Table of content should be used just to override properties of the ArcMap table of content or add new properties. It is not recommended to explicitly configure the whole table of content in WebOffice 10 R3 again. You would do the work twice (it is already defined in the ArcMap table of content)!