Best way to keep 2 external USB harddrives in synch

Automatic on a timer - Cobian Backup

Manual when you want to start - Microsoft Sync Toy

FreeFileSync (http://sourceforge.net/projects/freefilesync/). Faster than Sync Toy. Open source. Updated frequently. Has an associated utility that constantly checks for updates to one hard disk (or directory) and mirrors those changes to the other. (Yes, I know I'm answering a three year old thread, FFS was around then, and was a superior choice then, and is a superior choice now.)

You can set it to run a preset task at a scheduled time using Windows Task Scheduler, by the way.

edited 2017-02: Another great program is Bvckup2 (https://bvckup2.com/). Turn off the archiving feature and it will just mirror C to D. Will run on a schedule. It's not free though.