When you run a permanent network, you definately want female connectors on each end, connecting the nodes with patch cables. That way, if a patch cable gets run over by a chair or you want to reconfigure the topology, it's just a matter of switching a few patch cables around. A patch panel is the coreward termination point, whereas RJ-45 faceplates are the edgeward termination point. If this doesn't make any sense to you, look at my crappy illustration instead. :)
P.S. - Though it's not included in my cheap diagram, a patch panel is usually mounted in a rack!