Is it possible to have multiple FTP sites on Windows Server 2003 R2 that bind the same IPAddress, but resolve based on name? e.g. ftp1.domain.com and ftp2.domain.com bind the same IP, and IIS resolves to correct FTP site using the domain name.
For your 2003 server, this will not be possible.
The virtual host name feature was introduced in IIS 7 and, therefore, will work on Windows 2008 Server or later. If you do upgrade (or have a 2008 or later server you can use), you can learn about using the virtual host name feature for FTP