The good news is that this was brought up in a different thread. Kovid mentioned that he intends to revamp the GUI server...although I'm not sure what will be changed. I certainly hope it will have the ability to serve multiple libraries. I'm also not sure of WHEN he will get a chance to get to it, he's pretty busy.
In the meantime you can use the CLI as Chaley mentioned. You'll need a little understanding of network ports and possibly port forwarding.
Cheers,
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