As a root folder create a new folder in Windows Explorer, like C:\QV_ServerRoot. In the QMC mount this folder as your root. QlikView server stores the PGO-files in this folder.
The second step is to mount the folders where your QlikView documents resides. For this use the “mounted folders” part in the QMC. It’s a good idea to use separate folders for the data extractors and dashboards. The mounted folder for the dashboards should be browsable and the data extractor folders not.
In your case (example for the commercial apps) you get the following folders:
In the QMC the data extractor folder is mounted with the option browsable off and the dashboard folder is with the browsable option on.