What OS are you on?
If its a Mac then its based on *NIX and will likely have a command called rsync which is a very clever way of synchronising data from one location to another, be it one directory on your HD to another on an external HD or two computers of the net.
Fire up a terminal and see if the command rsync is installed by typing it and hitting return if so you should get all the options printed out. Let us know if you want some examples but something like...
rsync -avz /home/cofe/* /mnt/usb/.
...would copy all the files in the directory /home/cofe/ to /mnt/usb/
The smart thing about rsync is when you come to do this again. It checks to see when files were last modified and will only copy over from /home/cofe/* to /mnt/usb/ those files which have changed, and the
really clever part is that it uses an algorithm (termed delta-transfer) to only copy the bits of the file that have changed (e.g. if you've edited only a section of a picture then only part of the file that relates to that will have changed, so only that will be copied over/updated).
If you're on windows you can get this feature by installing a UNIX-like shell called
Cygwin which I (naturally!) find very handy when I have to use Windows computers, just make you select the rsync package for installation if you're going to try this out.