Backing up SSD + HDD

[ProMod]

I have a 120 GB SSD + 500 GB HDD in my MBP. Time Machine backs up the setup beautifully, but I was also maintaining a daily bootable backup of my system with Carbon Copy Cloner before I installed the SSD. What is the best way to maintain that backup with CCC now? Should I just backup the HDD, which contains all of my data, and forget backing up the OS and apps on the SSD, or is there a better way? The only other thing I can think to do would be to add a new partition to the backup drive that's 120 GB and clone the SSD to it each day when the HDD backup runs.