Why would you be looking in /root? Aren't you doing most work as a user and only su'ing when you need root priveleges?
The config file should be ~/.Xresources, or in some cases .Xdefaults. Open that file and you can add lines such as
eterm*transparency:true
eterm*background:black
and so on. Man eterm should show you all of the options and what symbolic names to use in this file.