Can you give a little more details in what it is you would like to do?
Under system tab , tehre is a tab named Folder, where you can set up ur root folder and also mount othere folders .
You can also make your mounted folders browseable or unbrowseable.
There is no rootfolder when it comes to source documents, only source folders.
If you mean the application data folder, that is not a root-source folder and should not contain any source documents.
You add folder you want as source folders here: