Ubuntu ships with Unity, which is dependent on Compiz, which is apparently incapable of handling more than one graphics card at this time.
What worked for me was to completely rip out Unity, Compiz, and lightdm, and then install KDE. Alternately, just install kubuntu (which is just Ubuntu with KDE, a really great desktop environment that's been in development since the '90s, rather than Unity.) This done, you will need to install the 3D card drivers.
At this time, the process of massaging the drivers to do what you want is not intuitive and can be exceedingly difficult. (It is with nVidia, at least, which is puzzling since it works with zero effort in Windows.) You may have to be somewhat tenacious.