I recently installed Debian Squeeze (unstable) and am trying to set up a lightweight Fluxbox environment (I'm not a big fan of Gnome and KDE). For the most part, I have everything working fine, but I'm have one somewhat uncommon feature in my system - 2 monitors. This computer used to be a windows-box, so having the extended desktop setup was easy. While Linux is great, and having a window manager like Fluxbox such that I can not have meaningless effects taking up half my memory is also awesome, the downside is a somewhat less accommodating configuration stage.

All of the info I've been able to find on configuring multiple displays is through the use of multiple video cards, but my system has both monitors on the same board - one on the DVI port, and one on the VGA port. I suspect the multi-video method is for older cards that predate the capability to run more than one monitor off a single card.

From install, the monitors have always been cloned, though that's also the case with my bootup sequence, so I'm not sure if anything's actually configured or if the video card just defaults to sending the same image to all monitors.

In Gnome, I can go into the monitor options and set it to extend the desktop, but that isn't persistent between window managers, which suggests, to me, that I need to be focusing on Fluxbox configuration files to get it to work for Fluxbox. However, I'm new to Fluxbox, and I am having trouble finding documentation for this issue (like I said, the multi-display configuration isn't that common). Any suggestions on how to extend the desktop in Flux (or any documentation I missed that adresses this issue)?

You probably searched the wrong term . Try "multi head".

Direct remedy AFAIK (I hope ): edit (as root!) the file /etc/X11/xorg.conf and add the following lines:
If the file doesn't exist in /etc/X11 try "X -configure" and then edit (as root!).