Indeed, you can conbine the use of the AnnotationConfiguration object and mapping files. Here's a quote from the Hibernate documentation:
Note that you can mix the hbm.xml use and the new annotation one. The resource element can be either an hbm file or an EJB3 XML deployment descriptor. The distinction is transparent for your configuration process.
Alternatively, you can define the annotated classes and packages using the programmatic API
Miixing JPA Annotations and Hibernate Mapping Files in the Same Java Project Tutorial
What is the exact error you're getting? Can we see a trace?
-Cameron McKenzie