It threw me for a loop when a Cisco CallManager version of a SQL server was on an
abnormal port (not 1433).  It took me a while to find it, but if you want to
connect to a non-standard TCP/IP port from SQL Management Studio, simply connect to
the hostname then a comma with the port number.

Example:  MySqlServer.MyDomain.com,3821

I stole this information from here.