Don't use Carbonite.
Carbonite is the devil. It skips files, as the makers of Carbonite see fit, and it's virtually impossible to actually get Carbonite to do what they advertise, which is to actually back up all your files.
So, moving on: let's assume you're using an actual PC to host your files, not a NAS box. (NAS boxes don't have a keyboard or monitor, and they usually run a proprietary operating system.)
For straight-up backup, my favorite service is Crashplan. From what I'm reading, there is a FreeNAS plugin and a Linux version. It runs in Windows, too, so no matter what OS you're running on your server, you're set.
Just a note on that topic: uploading many gigabytes of data takes a long time, especially since cloud services tend to throttle your upload speed. It usually takes me several weeks to get my backup service completely populated with my current "important" files set, which is around 250GB.