It is vital to have a separate, project-specific place to sort your notes for a particular project. An outliner helps with developing a rough structure, but also allows you to keep it flexible. The structure of an argument is part of it and therefore will change during the process of developing it – it is not a vessel to be filled with content. As soon as the structure no longer changes much, we can happily call it a “table of contents.” But even then, it helps to see it as a structural guideline and not a prescription. It is not unusual to change the order of chapters at the very end.
outlines and thoughts for how stuff is to be put together is for individual(writing) projects and won't have value when you are done. this is scaffolding. it's okay to get rid of it.