Depends on what you are plugging into to it. BIOS controls all the basic functions.
CPU clock speeds
Memory speed settings
A whole host of boot options, including the primary boot device.
Nearly an endless list of options. But if this is a simple break/fix replacement most things should at least work with default settings. CPU should default to normal settings, Memory speed may need to be configured if it is faster than DDR3 2133. If you have a single boot drive, should be no configuration. If you have multiple disks or a non-standard boot config, that would be up to you.
Not much you can do from Windows with systems that old. The BIOS is there to be used, you don't really need another interface.
In Windows you will need to remove the old drivers for the motherboard and download and install the latest driver's from support.asus.com. It may be necessary to boot into safe mode to accomplish that first step.