Don't just explain how your system is built and what it does, also explain why it works and why it's interesting. Write for people, not machines. It's not enough that your argument be correct, it has to be easy to follow. Don't rely on the reader to make any but the most obvious deductions. That you explained how the frobnitz worked in a footnote on page seven is not a justification when the reader gets confused by your introducing it without further explanation on page twenty-three.
Formal papers are particularly hard to write clearly.
After you have written a paper, delete the first paragraph or the first few sentences. You'll probably find that they were content-free generalities, and that a much better introductory sentence can be found at the end of the first paragraph of the beginning of the second. If you put off writing until you've done all the work, you'll lose most of the benefit. Once you start working on a research project, it's a good idea to get into the habit of writing an informal paper explaining what you are up to and what you've learned every few months. Start with the contents of your research notebook.