Do I need to target the root of the destination HDD when using carbon copy cloner?
Carbon Copy Cloner essentially requires you to backup one Volume to another.

It doesn't have to be the entire volume, there are some quite comprehensive filtering options, but it does need to be to a distinct Volume, not just another folder on the same one.  

It's always wisest to have a full bootable backup, just in case, but single folder backup is actually possible.

A separate Volume on the same physical disk would be acceptable, though of course if the disk dies, it takes both copies with it.