You cannot save edits made to a subdocument from within the master document. Instead, you must open the subdocument, either by double-clicking on it in the master document’s Navigator, or by opening it from outside the master document. Then you can edit it just as you would edit any other document. Just one rule: if you make any changes to the styles while editing a subdocument, you must copy those changed styles to the template so they are available to all of the subdocuments and to the master document.
If you change the contents of any subdocument, you need to manually update the table of contents, bibliography, and index from within the master document.