По словам man xorg.conf,
When the Xorg server is started by the “root” user, the config directory search locations are as follows: /etc/X11/<cmdline> /usr/etc/X11/<cmdline> /etc/X11/xorg.conf.d /usr/etc/X11/xorg.conf.d where <cmdline> is the path specified with the −configdir command line option (which may be absolute or relative). Finally, configuration files will also be searched for in directories reserved for system use. These are to separate configuration files from the vendor or 3rd party packages from those of local administration. These files are found in the following directories: /usr/share/X11/xorg.conf.d Так /etc/X11/xorg.conf.d, где вы должны поместить свою конфигурацию, и /usr/share/X11/xorg.conf.dгде программное обеспечение будет помещать файлы конфигурации.