Yes! I do this all the time.
I mostly use CCC in two modes:
1) regular (hah!) backups of our laptops, I use CCC to clone to a disc image
2) when I swapped the HD out of my iBook (I also have a FW enclosure), I cloned the old HD onto the new HD first, then did the physical replacement.
The only thing you have to watch out for is how the OS "Blesses" bootable partitions. It is not sufficient to just copy everything over using CCC, You need to "bless" it to make the partition directly bootable. For instance, when I changed the HD in my PB, I wasn't able to get it to boot right away. I needed to plug in my old HD (The one in the FW enclosure, remember?), boot into the OS, and select the new HD in the System Preferences panel. That "Blessed" the drive and I was all set from there.
I think the newest version of CCC may have the option of "Blessing" the cloned drive that you make, but I'm not sure....