You might have the boot sector on the second drive, or a page file. Windows 7 can do that if you had both drives working during the install. You can check this by disconnecting that drive you want to format and see if windows will boot up on the drive your wanting to keep windows 7 on. If it boots o.k. then disconnect the drive your keeping and connect the drive you want to format and use the Ultimate Boot CD. There are several disk wiping programs you can choose from to wipe the drive with
http://www.ultimatebootcd.com/You just need to burn the .iso you download to make a bootable cd disk, set the bios to boot from your cd drive as the first device. Pop in the disk and boot up your pc. If you do not have anything to burn an .iso or have never burnt an .iso boot disk, you can get Image Burn for free
http://www.imgburn.com/