Cite While You Write always creates the initial bibliography at the end of the Word document that it has formatted. If you move the bibliography to a different location in the document, EndNote keeps it there even if you reformat the paper. You can drag-and-drop the bibliography, or, if Instant Formatting is disabled, you can Cut and Paste the bibliography.
Note: When Instant Formatting is enabled, use drag-and-drop to move a bibliography, not Cut and Paste. If you try to use Cut and Paste, Instant Formatting will create a new bibliography at the end of the document before you have a chance to Paste.