When you are in the VSC console within VC you can select which of the servers from Linked Mode that you wish to use. The location bar along the top that has like "Home > Solutions > NetApp > ServerName", if you click the server name you will get a drop down to select which of the VC servers you wish to use the VSC for.
Only thing you need to ensure is that you have access to the remote ports that VSC is running on from the workstation/server you are running the client from.
If you wanted a single pane of glass view for both VC servers inside the VSC then this isn't available as far as I know.
I was searching for some info on VSC today, and ran across this thread. I saw the new VSC 4.0 was just released, and checked the IMT out of curiosity. There's a note saying that "vCenter Linked Mode is NOT supported with VSC for VMware vSphere". I don't see the note on VSC 2.x, only 4.0. I don't know if there's a bug introduced with 4.0 or what.