Root Folder setting in Qlikview server where you define the location or a path of the folder where your qlikview applications are stored physically. Root folder is necessary cause for Qlikview to publish report it needs the report location.
Sometimes it happens that you have reports in some other folder residing at other location then the root folder location. In this case you will be defining the mounted folder and the reports from the mounted folder will be published to accesspoint.
Hope this will help you.