When you start your computer, a message informs you of the key(s) you need to press to enter the computer's BIOS setup.
One of the BIOS setup options is PNP OS (Plug and Play Operating System).
If you set the PNP OS option to YES, the BIOS only configures critical devices, such as video, keyboard, and hard-drive. If you choose this option, neither the BIOS nor Windows configures motherboard devices at startup.
If you set the PNP OS option to NO, the BIOS configures critical devices and all motherboard devices.
Generally, Windows will leave BIOS-configured hardware alone, even if the BIOS configured it less than optimally.