CCC can back up the contents of the Boot Camp partition, but it cannot make a bootable clone of the partition. If your goal is to back up your user data on the Boot Camp partition, CCC will meet your needs. If you're looking to migrate your Boot Camp partition to a new hard drive, you might consider an alternative solution such as WinClone, or one of the commercial virtualization solutions that offer a migration strategy from Boot Camp. CCC is not designed to accommodate backing up or restoring Windows system files or applications.
"Will CCC clone both my OS X and Windows partition at the same time?"
No, CCC will copy only one volume at a time, and CCC will not modify the partitioning of the destination disk. You should apply your custom partitioning prior to restoring anything to your new disk.
"I'm migrating to a larger disk, will CCC work for my Windows volume?"
No, CCC will not create a bootable backup of your Windows volume. Creating a bootable backup of OS X is mostly trivial. For Windows, there are numerous tweaks that have to be made — you must update the boot sector of the root target device to point to the correct start sector of NTFS volume, the boot.ini may need to be updated with the slice number of the partition, you have to restore the MBR, you must synchronize the GPT and MBR partition tables. Windows Vista+ has yet more requirements.
"Will CCC copy my Parallels/VMWare virtual machine containers?"
Yes! These are just ordinary files as far as CCC is concerned, CCC can copy these just fine. Note that these files can be quite large, so occasionally problems are encountered when these files are in use or when the destination volume does not have sufficient space to accommodate the updated copy of the VM container file. These two sections of the documentation address these matters:
Can I run a backup while I'm using my computer? If I have open files, will they be backed up?
"My destination has exactly enough space to accommodate the data on the source, why can't CCC complete the backup task?"
Example pre and postflight shell scripts (e.g. how to automatically suspend Parallels)