You can't use a 'spanned' video mode over displays that are on separate physical cards.
With two separate cards, you can display overlay-based videos on both monitors simultaneously (with one card, it can only be on the 'primary' unless you run in a spanned mode), or run one 3D-accelerated application on each at once.
Beyond that, they work pretty much the same. Windows doesn't care whether the monitors are on the same card or not in terms of just running its GUI and letting you drag windows around.