I'm one of those weird folk who run three monitors, and even though 12.04 promised better 2+ monitor support through Unity 2D, I still find it lacking. Perhaps it's the way I have it configured, but I use two nvidia cards with xinerama, which means I'm forced to use Unity 2D (no compositing support). Unity 2D just isn't as stable or usable. I really, really hope they put more effort to fixing this in 12.10.
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.