An important goal of your graduate work is to try to get papers published. Here is an idealized procedure.
Write your paper as a LaTeX article.
Divide it into sections with \section,
and include appendices and bibliography.
Migrate that paper into the larger body of your thesis
as a \chapter.
If the chapter has an abstract, move it into a chapterabstract environment. See Section 8.1, “The chapterabstract environment”.
If the chapter has an acknowledgement, move it to a
chapterack environment. See Section 8.2, “The chapterack environment”.
If the chapter has appendices, enclose them in a chapterappendices environment.
Begin each appendix with a \section command. See Section 8.3, “The chapterappendices environment”.
For the chapter-level bibliography, use the chapterbibliography environment. See Section 8.4, “The chapterbibliography
environment”.