When configuring ArcGIS server and the GIS Server Directory locations do the folders themselves get created when creating a new site in Manager? Also at what point is the arcgisserver folder created?
Only the default parent AGS folder is created for a new site. You would need to create subfolders off this parent folder, but you can only create 1 level of subfolders in AGS. I believe the arcgisserver folder is created when you install the AGS software.