No additional setup was necessary.
As previously posted, Catalyst doesn't always see the cards correctly if the sources (camera feeds) aren't connected upon launch of Catalyst. In addition, the Catalyst Control window seems to need to have Video Input 1 deselected, then Video Input 2 needs to get assigned to Card 2, THEN re-select Input 1 and assign it to Card 1.
This is with an older version, so Richard may have fixed some of these issues already. Your mileage may vary.