Use something like Partition Magic and format that drive as a Linux partition. If it's unformatted or it's not based on the NTFS, you wouldn't need to do that, just load the drive in windows and resart the computer with the cd in the tray.
Then you would just load up the linux CD's and when you get to the part where you choose the section where you choose what drive to install it on, just select that drive and continue the install
Just do NOT install LILO (the LIinux LOader) in the Master Boot Record area of your hard drive. Linux can handle booting from other means, windows cannot. The floppy disk boot method is your safest option to start with.