Use the slip-box approach to write a paper

Take notes whenever an idea pops into your mind.
Ensure you always have something on hand to take these notes. You can type them on your phone, use a voice recording app, or just write them down in a notebook.

Make notes about the literature that you are reading.
Whenever you read a book, make notes about the content, which could help you later in your own work. Be extremely selective about the content and the quotes that you choose to write down; select only those you do not want to forget.

Make notes for your slip-box.
Go through the notes you made in steps one and two, and write down your thoughts and ideas about them. Think about how they can help you in your research and their relevance in this context. These are your permanent notes to be stored in your slip-box, which is just a regular box used to store your notes for easy accessibility later on.

Link your notes to each other by numbering them appropriately.
Add numbers to the notes to link related notes and file each note behind one or more related notes for easier accessibility later on.

Develop your topics, questions, and research projects through your notes.
Go through your notes to see what questions and arguments arise. Repeat the above steps to take more notes and strengthen your arguments. Look into the chains of linked notes to see what ideas have already been developed.

Turn your notes and ideas into a rough draft.
Bring all the related notes into your workspace and start writing. Translate these notes into coherent words and sentences and embed them in the context of your argument.

Edit and finalize your manuscript.
Once you have translated your notes into proper paper, edit and proofread your document. Detect flaws in your argument and correct them through your notes.