I use Qubes with several secondary screen configurations but in XFCE 4.12 there is no “advanced” tab in the display screen settings and I can’t save each configuration. I wonder if it’s possible to configure this from the command line but I’m afraid to do something stupid.
XFCE is a window manager for Linux in general so there’s nothing specific here about Qubes. This means you can search on the web for “save XFCE screen settings” and most likely someone somewhere has already written an answer for that. Just remember that the terminal in which you type any solution is the dom0 terminal (XFCE Terminal).