The Kindle allows you to upload documents via USB by simply placing them in the /documents directory or any of its subdirectories. However, there is no way to navigate this hierarchy on the device itself. KSync is a simple python script that simulates that feature by creating a collection for each subdirectory in /documents.
Run KSync to write a new collections table to the Kindle.:
$ ./ksync.py /Volumes/Kindle
In order to make the Kindle recognize the new collections table, you need to unmount it and then do a hard reset by holding the power switch for 15 seconds.