To make a backup of all my partitions, I use a proggy from Aminet called "Mirrorcopy". It copies files from the source to the destination ONLY if:
a) They aren't on the dest., or
b) they are there but have changed
It also removes files from the dest if they have been removed from the source. This way, the 2nd drive is a "Mirrorcopy" of the 1st drive.
You can do this on an automatic basis by using another program to call mirrorcopy: also from Aminet, it's called EZCron. Leave your miggy running overnight & it will automatically backup.
NOTES:
I have found over the years, that mirrorcopy will fail & stall without leaving an error message this way. It's worth doing it manually every so often to check it, and make any corrections which can be found by doing it manually.