just run 2 copies of X, one for each monitor. Then put 3 virtual desktops on one side, and 3 on the other.

Your suggestion gives me 3 possible pairs of virtual desktops up at once. This gives me 9 out of the 15 desired pairs of virtual desktops up at once. Any time that I'm interested flipping between the other 6 combinations, I'll be cursing away. :-/

Cheers,
Ben