Back up hard drives don't match

I store all my software on the iMac internal drive, and use an external 500GB drive to store all my music, photos and movies. I have another 500GB external drive that I (try to!) use to back up the primary external, but somehow I seem to have a mismatch between the two external drives.
I haven't used cloning software before, just manually drag and dropped files over. terrible practice I now realize, because the number of files in each drive doesn't match.
I'm worried that if I clone one of them that I may loose data on the other if it has files that aren't on the primary.
Is there a way of checking which files don't match between the two drives? I have a third external drive now, and am thinking of cloning the primary external to it, then trying to work out what files (if any) on the old back up external need to be copied over to it....basically trying to start fresh and use cloning software for backing up going forward.
anyone able to help with how I can identify the mismatch in files on the two drives?

Perhaps synchronization software such as ChronoSync would be a better choice for you than a utility that only makes a clone from one volume to another.
Regards.

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