Hi
first if you have onboard graphics and want to install a pci express card you will need to go into set up when your computer first boots up, ie press del when you are in set up you will need to disable onboard graphics, once you have done this you must press f10 to save to bios, reboot the system and when it goes into windows it will appear as big graphics, change the resolution to 800x600, then unistall the drivers for the graphics card, switch off the machine install the new pci card, its the same as installing an AGP card, just plug it in and reboot, the computer will then tell you it has found new hardware, you know the rest on how to install the software.
As for the pci express16 cards, they are better than agpx8 as they run at double the speed and bandwidth, and if you get a good 512mb card like I have you will see the difference straigh away. when playing games and stuff like that. if you wanted to look at the difference between agpx8 cards and pci express16. first look at www.xfxfoce.com and the country you are in, you can see all the specs about the cards and what speeds they run at.