when the computer starts ,the bios looks for the hardware attached like cache,memory ,hd ,cdrom etc and then using the booting sequence decides where to look for the code which will load the os .this code is stored in the first sector of the device .
in case of Windows NTLOADER loads the os,boot.ini file is used as the configuratin file.
in case of linux lilo /grub or other loaders are used
these loaders use configuration files to locate the kernel and decide the root file system