Because Refworks can handle references (citations) for all of your classes and papers you will want to manage your references by creating folders for each class or research paper.
Creating a New Folder
You will then see your folders displayed in the left column under the folder icon in RefWorks. You can then add references to your folder(s).
To add unassigned citations to folder select the unassigned citation and click the folder icon on the top row.
Add the citation to the desired folder.