There have been many books dedicated to helping new users to use MS-DOS commands. Instead, this manual's goal is to simply familiarize the user with what they should know. MS-DOS uses a heiracrchial organization of directories to store its files .
Files are anything that contain data.
Word processing documents, spreadsheets, saved e-mail messages are all examples of files. A directory is a place where files are collected. Generally the files in a particularly directory are contained there because they share some common theme, i.e. all word processing files are in one place, spreadsheets in another. A good analogy is to think of a phone book. The people and their numbers can be considered files and the phone book can be considered the directory.