Organize your front matter. The title page, dedication (optional), table of contents, list of illustrations, foreword, and preface are all considered front matter. Sometimes a publisher will want these as separate files. Create your table of contents after everything else is completed.
Insert your main text, chapter by chapter. In general, publishers want chapters labeled, but they do not always want the pages numbered. Chapters are organized into topics and subtopics, and each is sequentially numbered. Indicate where in the main text your illustrations, tables and figures should go, but save them as separate files.
Attach your end matter. The appendixes, endnotes, glossary, bibliography, index and author biography may need to be sent as separate files. Your publisher will offer specifics for each of these parts. Generally, you can put each of these parts on a new page, instead of including them as a running text.