First, all credit goes to Dustin Riley for this article. I have simply copied and pasted it for archival reasons.
The original article can be found here: http://blog.dustinriley.net/2010/03/12/binding-multiple-ssl-sites-to-same-port-in-iis6/
If you attempt to create multiple sites in IIS6 that use the same SSL port (by default 443), then you will get an error message when you try to start the second one stating “IIS was unable to start the site. Another site may already be using the port you configured for this site. Please select a unused port for this site.” To setup SSL on the second site you need to either use a different port or edit the metabase directly. IIS6 comes with a script that will allow you to edit the metabase and add the binding for the second SSL site
The script is located in the Inetpub/AdminScripts directory and will need to be run from there in the command prompt. You will need to know the site identifier for the site you want to add the binding to. You can find this in the IIS Manager, drilling down to Web Sites, it will be in one of the columns in the right pane.
cscript.exe adsutil.vbs set /w3svc//SecureBindings “::”
cscript.exe adsutil.vbs set /w3svc/1/SecureBindings “:443:server.example.com”
Once you complete this you should be able to start the site in the IIS Manager.