First of all to insert 2 video cards into one PC, you'll need something called an SLI motherboard. Basically it allows for two PCI-E slots to install 2 cards at the same time.
These can be used for two purposes (theres usually a switch on the motherboard).
1 is to use it to use up to 4 monitors at once on one computer, with 2 working indepent from one another.
2 is to use it to play games in a few settings (some are for older games, and some work on games better than others)
For example one setting would be to have 1 video card render the top half of a screen, and the other video card to render the bottom half. This would half the time it takes to render a frame, and so speed the whole process up, speeding up a game.
Another setting is to have it set up so that each card does a frame each and then sends each one to the monitor in turn, which can also speed games up. Though each game likes different settings.
Some games dont like SLI at all though (though most new ones support it) and so no setting will work, and it'll be like using one card.
So in no way is SLI something to replace a dedicated high end card (even though, two 6600GTs might beat a 6800GT, the fact the cards are working off each other, and only some games work properly on it, means that its not better than getting a dedicated 6800GT in no means (though might be cheaper), but is great for some games, and so would be worth while for example to get two high end cards and insert them together, maximizing performance.
The program is just basically the drivers that you'll install for the cards that you'd have to setup (using save slots) to work on a different setting for each game.
I hope this helps you