You can use the following URL/username/password to have Tomcat (uPortal) start HSQLDB in memory, while still being persistent across server restarts.
jdbcDriver=org.hsqldb.jdbcDriver
jdbcUrl=jdbc:hsqldb:file:/path/to/persistent/files/uportal.db
jdbcUser=sa
jdbcPassword=
The downside to this approach is you can't use an external tool like DbVisualizer (or similar) to connect to the database while it's running under tomcat.