JBPM5 uses "pojo model jars" and has a concept of a "package" which is the way you bundle up the processes and pojos together (I believe). You could probably build these packages outside of your system, and have your code load the package into your app from a file or other location.
If you use persistence, you do not need to directly worry about what is in the database or how it gets there. JBPM5 will just "do it's thing."