I do not know if you would consider something like a file synchronization tool. I used for a similar task : unison
(over the network, but I think you can do it between two directories also).
So when you plug the usb, it will copy to it the newer files from your computer to the stick, the newer files from the stick to your computer and, in case of conflict, ask you what to do.
PS: but really, why not setting up a network ?