Create your secondary FTP account via your control panel and then use these settings to login:

FTP Server: Yourdomain.com OR YOURIP.
FTP Login: secondaryusername@yourdomain.com.
FTP Pass: secondarypassword.

A secondary FTP account has access to only one subfolder of your public_ftp folder. For example:

Secondary FTP Account: bob@yourdomain.com
Secondary FTP Root Folder: /home/yourusername/ public_ftp/bob/

If you would like to setup an FTP account for a subdomain, you need to use the same name for the subdomain and the FTP account:

subdomain: mysubdomain.yourdomain.com
FTP: mysubdomain