Have you resolved this issue? I'm having the same problem.
I also tried to do it myself starting from source, but it was too difficult for my skills.
I want to share my experience:
my application (same .jar) can run either (1) on thick client (container embedded), or (2) distributed server (Tomcat + container embedded), or (3) company servers (Tomcat + jboss as + ejb3). Ejb3 makes it possible!
I decided not to use multiple datasources (or databases) within solution 1 & 2. This is not a workaround because every table can hosted by the same database as there are not scalability or performance issues. Doing so I get also a better manageability.
Where I need multiple database is within the third solution, where there will be lots of records.
I'm using mysql, so myisam performance gains are visible only within the third solution.
So, just think on what you really need.
In every case the original question is still open.