If I understand you, you want to be able to connect a USB device to the
standalones.
You *could* attach the USB controller to the standalone using the
"Devices" tab on the qubes Settings. I suspect that this isn't what you
want, and that what you want to do is keep the device attached to
sys-usb and pass it through to the standalone.
For Windows, there are Qubes Windows Tools, which provide *some* qrexec
functions, like inter-qube copy and paste. Unfortunately I don't believe
that the tools currently support USB pass through. So the only option
would be to attach the USB controller. (I'm not a Windows user.)
For Linux, this would depend on what distribution you have used for the
standalone. You haven't said. If it is one of the stock qubes distros
then you *may* be able to install qubes packages and have them work -
note that "may". The best bet would be to create a standalone from an
existing template.
I don't understand your question about executing a standalone as root. If
you mean "can I run as root in the standalone" the answer is "Of course"
- how you get to do this depends on what distribution of Linux you are
using.