I always use rsync for backing up data.
Rsync with the switch “–delete” will delete the files at the remote end. Without specifying “–delete”, files at the remote end will not be deleted. As such the crux of your problem.
For example, so long as the drives are formated EXT and are not FAT/NTFS:
$ rsync -ax --delete /source_folder/ /remote_folder/
(FAT/NTFS formated drives will required a mix-mash of extra flags for omitting permissions, etc…)
Best backup practice is likely to use an external Firewire/USB-2/USB-3 hard drive. Even better, put a NAS in your garage in the event your house catches fire, but then you’re likely using a slower gigabit wired network.
The current costs of commercial remote storage is probably not feasible with the data accumulated with RAW images. But that’s just my opinion.