Because I cannot grant permissions by using options in that panel, I actually must use cacls.exe to set my folders' permissions, with an irritating DOS windows which is poping each time a permission is set...

If the folders are installed by your application, then the permissions are not replaced but rather set. If this is not the case, I would say that it is not a good practice to modify the permissions for folders or files that are not installed by your application.I think that it is not a good practice to completely replace the existing permissions by the new ones...