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