Hi Amulya,
If you are using EasyDMS autumatically Document Structure is created (FOlder>SubFolder>Documents...). If you are creating DIRs in SAP GUI, you have to assign it into Document Structure by using t-codes CV12.
FOr Deletion of Originals, provide users only Display access.Because in the standard the users can always delete originals if they have change authorization for the document info record and there is no specific object just for handling the original files.At the moment I can only recommend you to create your own authorization check with the help of BADI DOCUMENT_AUTH01.
/Tilak