xterm is just a window which gives you a command line. The xterm application is launched from the user interface, which is executing as the 'user' account (non-admin), and all applications launched from one account will be of the same account (user) unless special measures are taken (which is not the case for the xterm app). In other words, xterm gives you a command line for the 'user' account. In order to change to the 'root' account you have to run another privileged command from the command line, and to get that you would also need to install the 'becomeroot' package. But you don't need to be root (=administrator) to make a backup of your home directory or to write to the SD card(s).

To execute the backup command described by gnuite you must:
1) Install osso-xterm
2) Launch X Terminal application from the menu (it'll be in one of the submenus after installation of osso-xterm)
3) Enter the command (cp -r .... as described by gnuite) and return, using the keyboard that'll pop up when you start X Terminal.