You can use the same objects/class in both JAXB and JPA. You can include annotations for both JPA and JAXB to map the same class to both XML and a database.
EclipseLink supports both JPA and JAXB in a single product.
This depends on what data you are sending through XML and to the database though. If the data is very different, then you may wish to have different objects. If there are no major differences in the data, then since both JAXB and JPA allow configurable mappings,
you should be able to use both.
See,
http://wiki.eclipse.org/EclipseLink/Examples/MOXy/JPA