If you have such an option, always leave it set to auto. There is no reason to be messing with the voltage of your AGP card.
If it is working fine, why do you want to do anything with the voltage and what prompted you to even think of doing anything with the AGP voltage.
I dont know where you read that from, but it is very untrue. No need to set AGP voltage. Some older mobo's need to have the AGP/FSB divider set correctly. This assures that no matter what the FSB is running (66,100,133) that the AGP bus remains at 66Mhz. AGP apeture size should be left at default (usually 64MB) unless you have a problem in that area.