I have about the same problem, but since I don't use KDE or Gnome I don't really use those control centers...
In Fluxbox I added a menu entry which starts the following command:
setxkbmap be
which sets my keyboard map to Belgian layout.
But I agree on using the KDE control center (or the button on the Gnome panel) when using those desktopmanagers ...
EDIT:
while fiddling with XF86Config I noticed an option to do this too ... (stupid me, should have figured it out earlier
)
in the keyboard's InputDevice section, add this line:
Option "XkbLayout" "be"
to get the same result ...