Should I justify the organization of chapters and sections in the research paper?
If I take your question correctly, it sounds as if you don't know whether to refer to the styleguide that informed you to structure your thesis in a certain way. So, in your introduction, you have a section such as:


  The next chapter of this thesis describes the background literature. Chapter 3 outlines the methodology and so on. Chapter 4 presents the experimental design, whatever … Finally, chapter 7 concludes and provides further possibilities for research. This structure is suggested by Cresswell (19xx)


If that's what you're thinking, then I would say no; don't reference the styleguide that you based your thesis structure on. Just like you wouldn't cite, for instance, the AP styleguide for your spelling conventions.