In FileMaker 11/12 running on a Windows Server, there are a multistep process to get CWP and IWP to appear for multiple domains.
Cliff nnotes version...
In IIS Manger:
> Create Site
> Add a virtual folder names jakarta
> Add a virtual app named fmi-test
> Map the FM Web Publishing ASAPI filter
The big question now, is what does this look like in Server 2012, IIS Manger, and FileMaker 13. There are a ton of URL redirects that I'm hoping will provide the 'magic', but I have not been able to find any docs on the topic. I will be working with this for the next few days, but I would welcome any help from others which are trying to do the same thing.