The AGP slot allows greater bandwidth and therefore speed but I don't know the technicalities.
PCI cards seem to be rare and often expensive for what you get these days. The AGP slot is normally brown and not as wide as a PCI slot. If you have the motherboard manual then it should tell you in that. If you don't have a manual then if you know the make and model number there's a good chance you can track it down on the Manufacturers site.
You have to be careful with the voltages as they changed sometimes when the standard was improved so you need to know, that if your motherboard supports AGP, what voltage it supplies.