As long as your using WinME or later (2k,XP) it should work. I've come across certain cards that didn't work together but it was always a card incompatability and using a different card with each allowed them to work. I've never setup a dual card system using an onboard video card but I wouldn't see why it wouldn't work. Once you install the second video card, go into your display settings and you will see 2 monitors, by clicking on each you can set the display properties for each as well as arranging them (one on top of another, side by side, etc). There is also a button to expand your desktop onto the second monitor, which you'll want to click.
One problem I've had with setups like this and games is that any game you use the mouse for which doesn't support the dual monitors will be difficult to play since your mouse won't stop on the side of the screen where the second monitor is located, it will keep on going onto the second screen. It's difficult to describe but if you play any game where you use the mouse to scroll around you'll notice it right away.
PCI video cards are all over, you can do a search at
http://www.pricewatch.com