Have you tried Gnome? I also use 2 monitors, and hope that Gnome on 12.04 supports multi-monitors well.
Unity has great support for multiple-monitors. Many, if not most, of the problems are due to: X, the video card drivers and Xinerama.
I always disabled Unity until now, precisely for the reason that it didn't work for me on this laptop that is often docked with 2 monitors.
All you need to ensure is you have decent video card/drivers