Don't use FTP to access anything besides the user level stuff inside /home. Because ftp is a very insecure protocol; anyone can read passwords sent in plaintext over the 'net. And since you'd need root access to be able use FTP outside of the home directories, you'd be passing your root password in plain text, for anyone to see it. Additionally you probably can't easily so configure your system because ProFTDd is designed to protect you.
You should use SCP (Secure CoPy) to upload/download other directories on your server. You can get SCP clients for Windows, Apple, Linux.
Jeff