This BIOS feature allows you to select whether to boot the system using the AGP graphics card or the PCI graphics card. This is particularly important if you have AGP and PCI graphics cards but only one monitor.
If you are only using a single graphics card, then the BIOS will detect it as such and boot it up, irrespective of what you set the feature to. However, there may be a slight reduction in the time taken to detect and initialize the card if you select the proper setting for this BIOS feature. For example, if you only use an AGP graphics card, then setting Primary VGA BIOS to AGP VGA Card may speed up your system's booting-up process.
Therefore, if you are only using a single graphics card, it is recommended that you set the Primary VGA BIOS feature to the proper setting for your system (AGP VGA Card for a single AGP card and PCI VGA Card for a single PCI card).
But if you are using multiple graphics cards, it is up to you which card you want to use as your primary display card. It is recommended that you select the fastest graphics card as the primary display card.