An application is normally written to work with just one database. Subsonic is written to store all information in HSQLDB. To make it store information in another database, you have to alter the source code and build a new release.
During the last year, I've been working from and to on a Subsonic server that is more oriented towards music. I'm not a big fan of HSQLDB so I store all library metadata in PostgreSQL, but I still use HSQLDB for user settings. If that is useful to you, it's all open source, and you can read about it at
http://dilerium.se/musiccabinet/.