Welcome to the Apple Support Communities
Unfortunately, you can't back up the Windows and the OS X volume with the same app if you want a reliable backup. You can try to back up both partitions with Time Machine if you want to, but you won't be able to restore the Windows backup.
I recommend you to use Time Machine or Carbon Copy Cloner to back up your OS X volume, and use WinClone to back up the Windows volume. With this, you will save headaches when you want to restore files in Windows