You should back up your Windows partition while booted into Windows, using Windows-compatible backup software, and you must backup to an external drive that is NTFS-formatted, whether it is over Ethernet, USB, FireWire or whatever else you can work out. Do not try to use a physical hard drive that has one partition formatted for Mac or Time Machine, and another partition formatted for NTFS. Use a completely separate hard drive.
Don't try to back your BootCamp Windows system up using Mac OS X outside Windows. You might figure out how to back up some files, but you will not be able to create a bootable "bare-metal restore" image, like those people in Windows-land call it.
Windows Vista and Windows 7 have a good built-in Backup utility that can make a full disk image for a full restore, but only to a hard drive that is NTFS-only. They can also do incremental/differential file backups in a separate procedure. And there are many third-party backup software solutions for Windows, such as Acronis.
Trust me, you will not want to try to do this using an Apple Time Capsule or a drive that has a partition that is formatted for Apple Time Machine. A couple of years ago I actually worked out a procedure for doing this using unsupported features on the Time Capsule, and I regretted it, because it interfered tremendously with my Mac Time Machine files when I needed to do a full restore on my Mac partition on my MacBook Pro.