If you have the EMS Folders add-in installed in Outlook you will see a folder called "ND-Send to NetDocuments" in your Mailbox. Under this folder you should see the Folders/Workspaces that you have in your NetDocuments Account. When you add a new Folder or Workspace in NetDocuments, in order for it to show up in Outlook you will need to refresh the folder above it by clicking on the name or icon of the folder. This will refresh the folder and its subfolders by retrieving them from NetDocuments.
For example, if I added a new workspace to my Favorite Matters list in NetDocuments, I would need to click the name or icon (NOT just the arrow next to it) of the Favorite Matters folder in Outlook in order for it to show up there.
If the above steps still do not work, you can delete the "Send to NetDocuments" folder and then restart Outlook (make sure there are no email messages left in this folder tree before you delete it). The folder will automatically be re-created after restarting Outlook.