|Most BIOS settings don't allow you to completely turn off the AGP bus but setting the shared memory to 0 or as low as allowed can be done.|
Because you no doubt have integrated graphics, that is the default graphics. In addition, your AGP and PCI cards can usually co-exist in harmony with both working. That holds true with an add in AGP or the integrated. There are some combinations that don't seem to work.
In order to get the PCI card to be your primary display you setup the dual display configuration with the PCI card as the Primary display. If you don't want to actually use both then at that time you can disable display 2.
To sum it up your PCI can't override the AGP slot. An add in AGP card does disable the integrated AGP graphics.
Hope I have made this clear.
The point made concerning the expected performance of the PCI card is valid.
The AGP bus was developed due to the restraints of the PCI bus. Total bandwidth limitations and the sharinging of those limited resources. The original version of AGP (1x) was still better than running a PCI card. The reason is the frequency is double and the bandwidth is exclusive.
You may have gotten confused by the name PCI. The newest video cards have a PCIe interface which sounds similar but is not the same bus.