RefWorks allows you to create different folder for various projects or classes. Choose the "New Folder" button under the "Organize and Share Folders" tab. Use the "View" drop-down to select "View Folders" to return to any of the folders you have created.
If you accidentally export the same citation to RefWorks multiple times, you can have RefWorks look for the duplicate entries and then delete them. When logged into RefWorks, go to the View menu and then click on Duplicates.
Select the duplicate entries and then click the red "Delete" button.