I haven't used SuSE a whole lot, but I'll take a stab at it.
The last time I had to mess with X video settings in SuSE, I found that as long as you don't mess with SAX2 (i.e. reconfigure using SAX2), it won't overwrite your xorg.conf file. Since I rarely use GUI tools to mess with my configuration files anyway, it didn't really bother me, but chances are, there's a better solution.
Here's what I would do. Make the changes you want to your /etc/X11/xorg.conf and back it up to something like /etc/X11/my.xorg.conf. Then find your "local" startup script/settings (try /etc/rc.d/boot.local) and add the following line:
cp -vf /etc/X11/my.xorg.conf /etc/X11/xorg.conf
This will copy your customized my.xorg.conf over the SAX2-overwritable xorg.conf every time the computer boots. Just make sure to make all your changes to the my.xorg.conf from now on.
Like I said, this probably isn't the best way to do it (I'm really much more of a Slackware/Gentoo guy), but I think it'll work. If anybody else has a better idea, please feel free to chime in!
Hope that helps.