If you want to keep your projects sealed off from each other, you can organize them into different Projects. By default, citations will import into the Project that you currently have open in RefWorks. Keep in mind that, while using the Write-N-Cite tool, you can only use citations from one Project per document.
To create and switch between Projects:
Within a Project, you can create folders to organize your citations.
To create and organize into folders:
Another way to organize citations is with tags. Imported citations will sometimes come with tags already attached by the author or database (be sure to select options such as "Author keywords"; "Index keywords", or "Tags" if available when choosing which information to export), or you can add your own.
How to add and organize by tags: