Where and how for library contents

I've been trying to figure out where I am supposed to put stuff like books and music files in my PE via USB.

I found the directory where the sample files are stored and I've added items in the downloads directory and they show up in the library, but after deleting some of them they still appear in the library, though they are inaccessible because the files have been deleted.

What is the proper method for adding and especially removing library content via USB, where should it be placed, and how do I get the device to rebuild the library database to reflect stuff I have deleted?

Thanks!