The only thing bad about having two monitors in Linux is fullscreen apps, from time to time. Mplayer for example is smart, it fullscreens to whatever screen it's on and leaves the other alone. VLC for example bugs out but at least it sticks to one monitor while doing so.
NWN is not so smart, and tries to run at an enormous resolution which either bleeds across both screens or takes up all of one screen and runs off the edge.
One solution is to run in windowed mode. This is less than optimal for all kinds of reasons, especially if you happen to have an auto-raising kicker or something similar.
Found this on the Gentoo forums though; putting a NULL into one of your MetaModes works:
Option "MetaModes" "1280x1024,1680x1050;NULL,1680x1050"
It turns off one monitor and leaves the other on.
CTRL-ALT-+ to switch to and from meta-modes, obviously. NWN recognized the smaller resolution and let me run at 1680x1050. Good old Gentoo forums, never let me down.