I had a similar problem like this not too long ago. I was working on an image upload script, and I could upload them, but couldn't work with them via FTP (delete, change owners, etc.). The way I worked around this was to use FTP to create the directories. Once the directories were created, I was able to manipulate the files.
The .htaccess I think is probably not necessary. I would use sessions to validate a user, and then just destroy the session when they leave, and make them login to upload the files. If you follow these steps, you will find that you can manipulate files via FTP if you need.
I would not use .htaccess, but would definately use sessions or cookies.
I'm not able to give you the FTP script I used, but it's basic PHP FTP functions that creates directories. Nothing special. If you need it, I can give it to you Monday night/Tuesday sometime.
~Brett