It really depends on what BIOS you have. Generally, you are not able to change the PCI.AGP frequency. It will automatically change when you change the CPU FSB. For example, in my BIOS, the frequency page looks somethign like this:
CPU Host clock: [Enabled]
CPU Clock: 
xPCI/AGP Frequency: [37/75]
The PCI/AGP bit is blanked out so i cant change anything.
Basically, your AGP and PCI frequency WILL go up when you start overclocking. You need to be aware of this, because if you start up your computer and it doesnt actually start, or crashes halfway through start-up, you may need to up the voltage in your AGP slot, so that the overclocked frequency can keep up with everything.
Although you wil mainly need to up the Vcore voltage of your CPU (to maybe around 1.75) and maybe up your memory .1v-.2v. Of course, dont up the voltage at ALL unless you have an unstable overclock, and be very careful when you do. Upping the voltage is what will destroy your parts if done incorrectly.