Oh.
Here's a general direction:
1) Allow FTP uploads (duh!)
2) Login, and call up the batch script (duh!)
3) Filter through the directory to see if there are any files!!
4) Count how many there are
5) Display a form asking where to put them (category, folder, whatever you want)
6) Move the files to the directory/category specified.
7) Re-examine the directory for any missed files.
That's basically what you'd need to do.
I'm sure if you look around, you'll find code on Listing files in a directory and Moving files.
Remember this: Keep the FTP upload directory and the final destination directory separate.
Hope I helped you figure out a general direction.
~Brett