While Time Machine is a great program, you might not want to use it or you might be splitting space on a hard drive with another family member. You could also use both methods, one for a comprehensive backup and another for a quick backup of certain files. This way you can organize your backups in a method of your own choosing – there is really no wrong way to organize a backup. Some teachers like to put all their lesson plans into folders by months or months within a year and back those up separately or gather all their presentations into folders by curriculum segment. It’s up to you. Whichever way you choose to do it, as long as you do it consistently, it is the correct way for you. You can group the files on your laptop and then copy them to the external hard drive or you can create folders on the hard drive and copy the documents to the folders. Again, it’s your call. The one thing you do want to make sure is that you see the green plus sign when you copy the files or folders over.
Also, it never hurts to double click on a random document you’ve copied just to make sure it’s actually there. Another way to check is to click on a folder on your laptop, hold down the Command key and hit the letter I (or while in Finder, click File -> Get Info) to see the size of the folder and do the same thing to the one on the hard drive to make sure they’re the same size.