You shouldn't need to change anything around in the BIOS really on installing a new drive if they're SATA, if you've messed around with the settings and it's not working as a result then my advice would be to reset it to its defaults. This is usually found as an option on one of the menus in the bios, if not then turn the PC off, open it up, pop out the CMOS battery (that's the round silver thing on the motherboard) and wait 10 minutes before putting it back in.
If it's IDE drives you're working with, then check the jumpers are set correctly for each drive (either cable select, or one as master and one as slave. There should be a jumper configuration pinout printed on each drive, if not have a look online.)
Once you've got both drives recognised, you'll need a windows install disk or a recovery disk - boot from that (make sure cd is selected as the first boot device in the BIOS) then follow the instructions through to wipe your drive (there's no data on it that you need right?) and install windows.