If library1 is on the physical server, and library2 is on the virtual server, then that command as it stands definitely won't work.
You would be, in fact, changing servers, and so yes, you would need to point the client at the correct server, which is best done using the access key. You would also need to make sure that the virtual server is visible on your network, to other PCs including your client PC.
There may be an additional command line parameter that will connect to the correct server and MC library. Have a look through this:
http://wiki.jriver.com/index.php/The_Command_LineI couldn't see anything obvious though. There is a /Connect that connects you to another host. That may work if Media Server is running on that host. Not sure. Try it.
C:\Windows\System32\MC20.exe /Connect m01p://virtualserver /Library MainLibrary2-VM [Don't ask me why "m01p". I guess that is the Media Server protocol?]
There is also the /MCC command and all the
MCC Commands, but I could see anything obvious there either.
Actually, it shouldn't be that hard, if the correct libraries are the default on each server, and the virtual server is visible on the network. Remotes and clients do it all the time.