Instead of 6 square virtual desktops, make 3 double-wide virtual desktops, perhaps? You would still have the issue of having to (somehow) run multiple views of the same application if you want to see it on both tubes at the same time, but it might reduce your desktop flipping a little.
Maybe you can get your boss to get you one of [link|http://www.digitaltigers.com/displays-atlas.shtml|these] and not need worry about it any more. ;-)
Cheers,
Scott.