I have been recently installed Debian, and right now I am trying to configure the screen to use the ratio 1280x800. The problem I have is that when I screwed up configuring xfree86 with
#dpkg-reconfigure xserver-xfree86
I was not allowed to start X because of invlaid parameters or something. So than I tried using
#xf86cfg
at the console and what do I know the screen is seemingly fixed by some sort of autconfiguration. The problem is though, that after I configured it, the screen still works only using the already existing paramters of 1024x768. So how exactly is it that xf86cfg can auto detect my screen size but not write into the configuration?

I'm assuming you're talking about a wide screen laptop. Try editing /etc/X11/XF86Config-4 .
The thing you need is the line:
at the end of section "Monitor".
also, if we're talking about a Presario R3000 series you might need to edit (same section):
to these values. I'm not sure if they work for other laptops.
After this, in Section "Screen", find the line "Modes" and put in there "1280x800" before any other resolutions. Hope this helps.
Katu