Website Hosting

I have a dedicated server (Ubuntu 12.10, Nginx, Proftpd) and wish to host 4 websites. FTP will allow me to log in utilizing root credentials only on the server's IP address; however, does not display any files even though they exist on the server. I have 4 FQDNs - utilizing 2 nameservers with 2 separate IP's. I have ISP control panel, where I set up 4 websites, DB's and user credentials. I set up virtual hosts for all the websites and they work properly. I cannot log into FTP utilizing these credentials or IP addresses even though they are setup on the server. I can only log in utilizing root credentials. How do I upload my websites to the server utilizing the individually created accounts corresponding to each website? Any help is appreciated.

You could shell in and do it.  Try removing Proftpd and install vsftpd instead; I switched to vsftpd and it solved my ftp problems.  You could also install webmin; it comes with a java based file manager; upload the files as a zip archive and then unzip on the server.