"root" directory can be used in two different ways. The first is the root directory for you hosting account, which usually refers to the place that your web host tells you to put your publicly viewable files.

The other root directory is the one for your Zen Cart. This is the directory into which you have installed your Zen Cart with all its sub directories.

The two roots are often the same, though will be different if you have installed your Zen Cart in a sub directory.