Well you need Windows 2000/XP for BootScan as far as i know.
Start the Simple User Interface and click settings button and select Schedule boot-time scan. If this option is grayed out or you have Win9x than you can’t use this function.

If you know the exact location of virus infected files,than you can use MoveOnBoot utility (freeware) to delete them at boot time:
http://www.snapfiles.com/get/moveonboot.html