HMC does not have support for multiple OWA sites. It has guidline how to setup default one, and how to setup Autodiscover to support multiple domains by redirecting incoming requests to single URL (this procedure is well documented in Exchange 2007 Autodiscover white-paper ;-).
Outlook Anywhere can be set for second (third, etc.) web site on the same CAS server by follow procedure:
1. Save Default Web Site config to XML file
2. On second web site create RPC virtual directory using saved configuration from step 1
3. Export configuration object for "Rpc (Default Web Site)" from AD to text file using ldifde. Object DN is CN=Rpc (Default Web Site),CN=HTTP,CN=Protocols,CN=CAS_server,CN=Servers, CN=Servers,CN=Exchange Administrative Group (FYDIBOHF23SPDLT),CN=Administrative Groups,CN=...
4. Update file to reflect name of the second IIS web site
5. Use ldifde to create new object in AD.