How to do correct prompt engineering?

How to make a proper prompt for a scientific paper? So that it is unique, anti-plagiarism - as if for an engineering paper along with footnotes

The exact same way you might instruct a junior human worker to do the task over a chat/messenger interface. Just explain to it very carefully and clearly what you need it to do, with as much specific detail as possible, and then check it does the job. Refine the instructions as necessary. If a task is particularly complex, try breaking it down into more easily explicable steps.