I agree- that whole desktop-bigger-than-the-screen thing bugs me, too.
You can get around it by making sure you either don't have a "Viewport"
section or commenting said section out (by starting the line with a pound
sign: Shift-3).
The other problem is that it sounds like you have 2 resolutions
Ed - In the /etc/XF86Config file, down near the bottom of the file,
is the "Screen" subsection. Within that subsection are definitions
for the various video modes. If you look at each, there is probably
a 'viewport x y' line. If you set the x, and y to both be 0, you
will disable the viewport
