I don't know about the best way to split things (I do it topically mostly, e.g. each website backup goes to a separate disc). But hashdeep is a great little too

I don't know about the best way to split things (I do it topically mostly, e.g. each website backup goes to a separate disc). But hashdeep is a great little tool for producing files full of checksums of all files that get written to the disc, and also for auditing those checksum files.