Because the Subsonic working directory is a SYSTEM wide java setting it is not possible to run more than one copy of Subsonic under one install of Tomcat.
You could possibly set up two instances of Tomcat and then do it that way, but they would have to be on different ports.
I just said NO, it is NOT possible under one instance of Tomcat.
You could COMPLETELY install a second TOMCAT instance and run it in there. But because the Subsonic home folder is a TOMCAT WIDE variable, one instance of tomcat can only host one instance of Subsonic.