Mac Pro :: Effect Of Two Video Cards

I have a Mac Pro and two video cards, and am upping the setup to a new Nehalem Mac Pro with the ATI 4780 card + NVidia GT120 card. For illustration purposes, I will use those two cards to frame my question, as we seem to be pretty familiar with their specs by now. My question is somewhat conceptual, and is difficult to explain, but I am counting on the MR collective intelligence to sort it out! I'll use a few scenarios to illustrate my point: Scenario 1: Heavy use of the 4870 card, using both outputs (two screens). Naturally, performance is better than using the GT120 card.

Scenario 2: Same heavy use, but this time one port from the 4870 is used, and one port from the GT120.

Scenario 3: Same heavy use, but both ports on the 4870 are used, and one port on the GT120 (three screens total)

Scenario 3: Same heavy use, but both ports on the GT120 are used, and one port on the 4870 (three screens total)

How do software applications deal with two video cards? Would running Aperture, FCP, gaming etc., degrade just one screen? Wouldn't the whole application have to slow down to accommodate the lesser card? Is there a "primary" card and a "secondary" card designation? I'm thinking of multiple monitor setups (three, for example) where a lesser card is necessary to drive the extra screen, but the application is using all three.