Gather the requisite tools to help you in your note-making process

Have something to write with and something to write on.
This will help you capture your fleeting thoughts and ideas easily. You can use a pen and a notebook, an app on your phone, or even a napkin. These notes are not permanent ones; they only serve as a reminder of your thoughts and ideas.

Keep a reference system to collect references and notes.
You can use programs like Microsoft Word, LibreOffice, Zotero, OpenOffice, and NeoOffice. These programs will allow you to store information about references such as author, year of publication, ISBN, and so on. A notebook will also work well if you prefer to write by hand.

Get a box (or an app) to serve as your slip-box.
If you prefer to write your notes by hand, you can keep them in a box. It can be any type of box, referred to as a slip-box, that can store the notes you have written. If you prefer typing your notes, you can use the Zettelkasten app, which implements the core ideas behind the slip-box approach.

Choose an editor with which to write your paper.
If you use Zotero to keep your references, it would be a good idea to use one of the supported editors such as Microsoft Word and LibreOffice. This will allow you to insert references without writing them out by hand.