I think I get it now, sorry, hehe
Have both drives in, including the one with windows now on, and go into Bios (usually Del at bootup)
Go into the second selection (Not sure exactly, because I'm on a college machine, and some are different)
Find where it says '1st boot device' and change this to the HD with windows now on (Thats what the bootup will look for first to boot to). Should be IDE1, or 2 depending on how the hard drives are set up... so just switch between.
The second boot device would then either be the 2nd harddrive or Floppy, CD rom drive, etc as a backup (The 2nd thing it'll look for if one fails for instance)
After making changes simply Save and Exit, and your done!
(This way of doing things is useful to speed the process of boot up, up, because some systems would be set up to look at the floppy, then cdrom, then finally the hard drive... It also means you can switch the first device to the cd rom, floppy, if ever you needed to put a disc in)
This should work, and it should boot up on the right one. Make sure the drive with windows is now a master though, and the other one is a slave, just so it doesn't confuse. It should work without doing that though.
I really do hope i've got it right this time. Sorry for the mess ups... I obviously didn't read it properly since the teacher was moving around the class
... I'm sorry about that though, and hopefully, you now have your answer