If you do not shape your traffic, then your network will suffer from slowness. Isolate the traffic to enhance the network performance which will effect positively on the enterprise application performance in a direct way.
For larger networks, it is required to have higher level of isolation and shaping, so routing (L3 network) is required and a different topology and routing protocol will be used depending on the network scale.
Where to be configured to guarantee the continuity in the service? It is very important to determine if to configure them at the switch or at the router and what kind of configuration to be used.
You can apply very complicated security until you loose the connectivity! Applying security rules require understanding for the policy and how the communication will happen between the points, then to apply the security in smart way.