Organization of your document involves both the overall structure of the entire paper and the development and coherence of individual paragraphs. In general, you want the reader to be able to follow your reasoning. The organization therefore should arrange the main points logically, while the design (headings and subheadings) should highlight them.
A document is unified when all of the information presented clearly relates to the topic. Unity may be strengthened by coherence, usually demonstrated by strong paragraphs with clear topic sentences and supporting details connected by cohesive devices. Cohesion results from using transition words to help the reader follow the writer's train of thought (e.g., "therefore," "however," "so that"), repeating key ideas in different ways (in this case, "unity," coherence," "cohesion"), maintaining a consistent style (using the same tense, point of view, etc.), and employing parallel structure (demonstrated in this sentence with: "using transition words. . . repeating key words. . . maintaining a consistent style . . . employing parallel structure").
"Paragraph unity requires that all sentences in the paragraph support a single controlling idea; coherence requires that it be clear, logical, and readily obvious to the reader how each sentence supports that idea" (Dr. Charles Glover, Texas A&M Professor of Chemical Engineering).
For more about paragraph unity, coherence, and cohesion, see the University Writing Center's article on Paragraph Construction.
A good guideline to remember when composing paragraphs or even a single sentence is that a general-to-specific pattern of organization usually works well both in the larger document and in its individual sections. For example, begin a paragraph with a topic sentence; then support that topic sentence with your main points of development. Conclude the paragraph and, if necessary, create a transition into the next paragraph or section of the report. When writing sentences, try to begin with a subject and a concrete verb. Writing this way helps your reader see your ideas clearly without having to hunt for your meaning.
Other resources useful for constructing coherent, unified paragraphs are Repetition v. Redundancy and the Claim, Reasons, Evidence template.
Headings and sub-headings help to unify a document while allowing your readers to quickly find the information they need. Headings and sub-headings are also markers to show how you arrange the material. Thus, your headings and sub-headings should clearly denote the content of the sections they are announcing. Your style sheet may prescribe how heading levels should be typed. If not, follow these general guidelines:
Use informative headings and subheadings
Not "Controversial Issues"
Instead "Reasons Why Big Data is Controversial
Use typography to communicate levels of importance.
For example, first-level headings could be bold or use a larger type size, while second-level headings could be in italics.
Use typography consistently throughout the document.
Additionally, if your document uses a general-to-specific pattern of organization, the heading and subsequent sub-headings should also illustrate this pattern of organization for your readers. For example,
1st-level heading: " Why Big Data is Controversial"
2nd-level heading: "How Personal Data Poses Security Risks"