Windows 2000 indeed has a design flaw that prevents this - but only on setups that run twin heads from one VGA chip. If you have two cards, all is fine.
There are drivers that circumvent this for one-chip multihead setups as well. Matrox's latest drivers bring their own control panel pages that let you set up two desktops with differing properties (however it's REALLY tricky to do if the 2nd monitor is not Plug&Play compatible, like workstation monitors with BNC cables). ATi's latest drivers, from how their control panel looks, can do it too - I haven't seen it myself yet, and judging from how many driver updates it took Matrox to manage, ATi's may or may not work.
The ultimate solution is to use Windows XP.
regards, Peter