That's the way mine are setup, my main drive (1TB Samsung) for both versions of Windows, my second (1TB Caviar Black) has a 600GB Backup partition (for Windows), the rest goes to Linux.
Do you have a backup of your main drive, and a bootable CD from which to access your backup? If so, and your boot disc was burned OK, I don't see the problem. With a working backup, you can reverse most any changes to your system.
I'd like to see you recover, but you need a working bootable CD to access your backup with. Without that, there are options, but they become complicated.
Cat