On footnote and citation format, consult and obey Kate L. Turabian, A Manual for Writers of Term Papers, Theses, and Dissertations , 5th ed. Your paper should make a single point or a handful of related points, and should follow a simple organization. Avoid cluttering it with extra points. If you developed an argument that later became ancillary as you rethought your paper, drop the argument from the paper. Break your paper into sections and subsections.
More sections is better than fewer.
Sections help readers see the structure of your argument. Label sections with vivid section headings that convey the main message of the section. Counter-arguments, qualifications, and limiting conditions of your argument. Start each section with several sentences summarizing the argument presented in the section. Writing such summaries is also a good way to force yourself to decide what you are and are not doing in each section, and to force yourself to confront contradictions or shortcomings in your argument.