The connections panel is what drives the switch fabric generation. In the panel you'll be able to make the following connections:
Master connecting to slave (memory mapped)
Source connecting to sink (streaming)
If you don't make the connection in the patch panel then no logic will be generated to create the data path between the master/slave or source/sink. Sometimes this is what you would want in you know that you don't need particular data paths (if you connect every possible connection you'll end up creating a lot of arbitration and multiplexer logic). Here are the SOPC Builder docs to learn more:
http://www.altera.com/literature/quartus2/lit-qts-sopc.jsp