One of my best friends Kjetil Lindløkken has done this in the Lync 2013 topology. The issue was how to get the Lync 2013 Enterprise Edition to use different instances for SQL server, and different ports.
As we all knows the default port is 1433 for the SQL and so does Lync 2013 also use at Default.
Well Kjetil found this out and has blogged about it here:
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