Computers will store folders and sub folders in alphabetical or numeric order. If you look (via windows explorer) at, for example, the C drive, you will see that is true. When you create your own folders, the same happens. In my case all my self generated data is in a "F" partition with a main folder : "My Documents" with sub folders such as My Photos, My Word documents etc. I use Freefilesynch to make a mirror image copy of the master folder on a regular basis, ensuring I have a back up of all my data.Because only a few files change, it takes only a very short time to synch.
I do use Auslogics disc defrag quite often. Please come back with more specific questions.