You can create a folder structure in the 'Files' section of a workspace. Simply click on the 'New' button and select 'Folder' from the drop down menu.
It will then create a folder in the current position. Click on the folder's name to enter the folder and upload files into it. You can create as many layers of sub-folders as required.
If you select folders by clicking on one or more of their check boxes, additional functions appear at the top of the list.
If you want to move a files/folders simply click the 'Move' button and you'll be presented with a list of workspaces (and the folders within them) - just select the Workspace (and sub folder if you wish) and then press 'Move files'.