Setting up different passwords for Filevault 2 and my user account I'm currently setting up Carbon Copy Cloner to create a backup clone of my SSD. I'd like to be able to store the cloned drive's Filevault 2 password in the keychain so CCC can access it to automatically do backups on a schedule. However, I don't want to store my administrator password in the keychain. (I've heard of a few exploits that allowed malware to access stored passwords).

Is there a way to set up a separate Filevault password for the cloned drive?

I'm running a MacBook 8,1 with El Capitain 10.11.6.
No, you can't have CCC be able to unlock a drive without storing those credentials somewhere.  The best you could do is create a new account that has the ability to unlock the drive and store those credentials instead, which unlocks the drive but not your primary administrator account.