Handbook of Writing for the Mathematical Sciences, 2nd Edition

At an early point in the writing of your paper you need to think about its high-level organization. It is a good idea to rank your contributions, to identify the most important. This will help you to decide where to put the emphasis and how to present the work, and it will also help you to write the title and abstract.
At the outset you should have some idea of the length of the paper. The larger it is the more important it is that it be well organized. However, it can be harder to write a good short paper than a good long one, for it is difficult to be simultaneously thorough, lucid and concise.
You need to decide in what order to treat topics and how to present results. You should aim to minimize the length by avoiding repetition; to obtain general results that provide others as special cases (even if the latter are more interesting); and to emphasize similarities and differences between separate analyses.
In addition to considering the first-time reader, you must think about the reader who returns to the paper some time after first studying it. This reader will want to skim through the paper to check particular details. Ideally, then, your paper should not only be easy to read through from beginning to end, but should also function as a reference document, with key definitions, equations and results clearly displayed and easy to find.