Gnome happens to know a lot about this. Mixing video cards is much like mixing spices. They work based on how they integrate with the other cards, the operating system, the motherboard and chipset. My personal experience has been that ATI's cards are somewhat picky. I find that Matrox and nVidia work well with a variety of different motherboards over the years for me.
When adding multiple cards, be sure to install them one at a time. That means you download the latest drivers before installing anything so that they are on your machine before you start. Then you open the case, install one card and start it up while it is still open and go through the process of installing the driver. Then you make sure that card is working and everything is fine. Then you shut down, install the 2nd card, run the OS again and install the drivers for the second. If there are problems, they will show up at this point. If they do, you might have to try a variety of solutions including removing the first card with its driver and then installing the second one first and repeating the process again.
When it comes to hardware/software conflicts, your video card will give you the biggest problems. Once you get that part going, then you should be in good shape. It is a lot like backtesting a trading strategy. You have to try a bunch of variables and see. I usually stick with nVidia because of the features of the drivers and the fact that one driver takes care of all of their video cards (unified driver). It simplifies things.
I hope that helps.
