It would be great, if I could define a Top level folder for each sandbox. For example: one permanent sandbox and a temporary on the RAM disk

Actually, you can, just use the FileRootPath setting!
P.S A question for tzuk, maybe I am just blind, but does the GUI not contain any way of editing the FileRootPath setting? Does it have to be editied from within the ini?

At the moment, only the Global FileRootPath setting is editable via the GUI. If you want to add individual sandbox locations, you have to manually edit the INI.