When I open my master document, Endnote puts a bibliography at the end of every chapter
Once you've completed entering your citations within your subdocuments, close your subdocuments and open the master.doc file. When expanded, this file will sequentially open and paginate all your subdocuments. From this view, you can then go to TOOLS - ENDNOTE (VER#) - FORMAT BIBLIOGRAPHY, and it should generate a complete list of references, that should appear at the very end of the master document (master.doc file). You then cut/paste the complete list from wherever it appears to the LIST OF REFERENCES section. You may then delete the references lists that appear at the end of each chapter. All subsequent updates to your references will appear in the new location.