In order to save all the Panes in the Docking control all you need to do is call the SaveLayout() method of the control.
Managing which Panes to be saved and which not is not a built-in feature in the current version of RadDocking and in order to save the layout for only specific Panes you will need to call the SaveLayout() method after which edit the generated xml and remove the unneeded Panes based on specific Headers or SerializationTags.
As we see you have posted about related issue in this post
, we have responded about that issue in that post where you can also find an attached project that shows how to save all the Panes of the Docking control as xml file or string.
the Telerik team