You don't need to clone them together necessarily. I run 2 backups 1 just for my Home account and 1 for my OS (SSD). Is that how apple sets up the SSD/HDD combos? I don't like Time Machine at all. Unless you are technically challenged or lazy it takes way too long to do what it does. Ever hit permissions issues on TM recoveries? Thats the kind of fun I'm talking about. "Your Copy failed for an unknown reason" Apple does not give you any feedback as to which file etc... No, Disk Images have never failed me, they are portable, bootable and can be managed by a ton of software.
Interestingly, I had done at least 8 restores to date from TM on multiple Macs and haven't came across permission issues. Been smooth sailing and relied upon.
I do use iBackup and Carbon Copy Cloner for other reasons.
If I wanted to do fresh installation ie. wipe clean, and reinstall each apps, I will use iBackup to help backing up settings, mail, iTunes and all data that's hidden away by application. It saves me time to dig in every folder and restore them. Just one click from iBackup and all those including, say, Mail settings, are back to where it is. Time Machine can't do this.
CCC is good during times I have to send my Mac away (e.g. repair) and have my cloned Mac with me. I can run it off another Mac just like my own. Then just CCC it back to my Mac when I get it back.