/etc/X11/X should be a symbolic link to your X server.
For instance, if your video card has an ATI Mach64 chipset, you should
run
ln -sf /usr/X11R6/bin/XF86_Mach64 /etc/X11/X
(if you had the XF86_Mach64 package installed; more on that
later.)
Edit /etc/X11/XF86Config with your favorite text editor.
For more information, read the manual pages for XF86Config
(man XF86Config) and your X server
(man XF86_foo), and the documentation in
/usr/X11R6/lib/X11/doc.