Sql Server Configuration Manager I have two SQL Server named instances, InstanceA and InstanceB on one computer, and they correctly show up under Sql Server Configuration Manager | SQL Server Network Configuration. 

However, when I try to configure SQL Native Client 11.0 Configuration | Client Protocols, there is no option to specify to which instance the setting will be applied. It appears that this is server (machine) level setting that would apply to every instance installed on it.

Am i missing something here? How to allow one protocol, say Named Pipes only for InstanceA and TCP/IP only for InstanceB? (without using aliases, preferably)

Thanks
You are confusing Server Network Protocols and Client Network Protocols. Essentially, Server Network Protocols change the way in which SQL Server listens for incoming requests and Client Network Protocols change the way in which an application sends a request to SQL Server. 

As the Client Network Protocols are a shared component and apply to all applications that use that library you cannot set a different protocol per instance that you wish to connect to.

Direct from the Client Network Protocols link below:


  At the simplest level, a SQL Server client can reside on the same machine as an instance of SQL Server. Typically, however, a client connects to one or more remote servers over a network. The client/server architecture of SQL Server allows it to seamlessly manage multiple clients and servers on a network. The default client configurations suffice in most situations.


More information regarding the two can be found in the links below:

Server Network Protocols

Client Network Protocols