In the iAnnotate Library, you can move your folders and files into new locations by tapping and dragging them. However, folders that mirror folders on a remote account (such as Dropbox) cannot have new files or folders added to them.

New folders can be created by tapping the blue folder icon with an orange plus sign on it, in the upper-right. You can move any folders or files into this new folder, however, if you move a folder (with files in it) that is mirrored on a remote account, you will no longer be able to synchronize the annotations you’ve made on those files to the remote server unless you upload the PDF individually.

Add a new folder

Other methods of moving files involve using the Split View or Breadcrumb Navigation in the Library. You can tap Split View under View Options in the Library, to display two panes at the right; you can drag and move documents or folders between the panes. Breadcrumb Navigation, with blue folders indicating your current location relative to the rest of the Library, also lets you move files or folders by dragging them into another folder icon at the top.