iTunes cannot locate missing files after I've moved them to a USB
do a search for your files, and in a finder window, drag them to the following directory where your iTunes file is located:

iTunes/iTunes Media/Automatically Add to iTunes

This will process them and put them back in your iTunes library.
You can move directories containing files as well, you do not need to sort your folders before, but if you don't like the way that iTunes automatically organize your files on import, you would have to reorganize.