When you install various applications into your website, often it will ask if you want to install as a "top level" or as a "sub-directory". Simply put, a "top level" means it is the first thing people see when they browse to your website.
For example, let's say your website is "www.domain.com". If someone browses to that, they will get the content you put in the "top level".
If you choose a "sub-directory" installation, for example installing WordPress into a "wordpress" sub-directory, then to browse to that application on your website people would need to browse to "www.domain.com/wordpress"
Why would I want a sub-directory?
We hope that helps! If you need assistance though, don't hesitate to contact our support team!