How do I Customize a Theme Correctly?

We don't recommend editing the theme or plugin files directly, not via SSH/SFTP or the WordPress file editor. The problem in editing a theme or plugin directly is that when a new version is released, it will be updated over the existing files and all the modifications will be lost.

We recommend making small CSS changes using a plugin made for that purpose, for example this Simple Header and Footer -plugin. Using a plugin makes sure that the changes are not lost when WordPress and its plugins or themes eventually updates.

If bigger modifications to the site theme are needed, the best practice is to make a child theme of the main theme as explained in the official documentation in wordpress.org

Another method of editing the site theme is to copy the theme directory and rename it. For plugins you have to change the version number to something artificially high such as 9.9.9. It should be noted that this method prevents updates for the theme to be installed.