The best way to accomplish most things is to begin with the end in mind. So before writing a word, first determine the end or purpose of your paper. Research papers make claims. Therefore, one of the most effective ways to begin a paper is to determine the claims that will be made by the paper.
Now with the claims in mind, you can decide what belongs in the paper. For example, the best way to prove a claim may be a figure or table of some results. For each claim determine what is needed to understand and believe the results in the figure. Most discussions that do not explain or prove a claim do not belong in the paper.
The above helps determine the content of the paper. Next, this content needs to be properly presented. The best way to determine the order of presentation is by incrementally building an outline. Start with a high-level outline, such as below.
- Related Work
Build up the outline. Insert the graphs that prove the claims in section 5 (as outline bullets–not figures). Add the content that is needed to understand and prove each claim in sections as appropriate.
Then iterative and refine. At this level (which is still bullet lists) it is very easy to re-order content. “Read” your paper; re-order content until the flow is perfect. You will likely find that important topics/concepts were missing as you do this.
Then add detail. At first the bullets in the outline are fairly coarse: sections, subsections, figures, etc. Keep adding detail until to get to the point where you, for the most part, have identified every paragraph that will be written. It is tempting to stop short of every paragraph, but it is important to take this down to the paragraph level. Up to this point you have not written any of the paper.
Next step: Write topic sentences. The paragraph is the basic unit of writing. Each paragraph should have a topic sentence: one, no more. If you cannot write a topic sentence then it probably is not a paragraph. It might be two or should be joined to another paragraph. I refer to this as an annotated outline.
If you follow this iterative process you will find that the writing goes very smoothly. You will rarely have to re-order large sections of text (which is never simply a cut and paste because the moved text is now presented in a different context requiring some editing). With an annotated outline, you can write the paragraphs in any order because you know the context of the paragraph. So when you feel the inspiration to write about transmogrification you can–and you will (probably) not have to edit it or re-order it later.
Last: Do not be pedantic about these steps. If you think of a good sentence or turn of phrase write it down lest you lose it forever.