Can someone please describe to me in detail how I can run these two versions in the same application?

It is stated in the migration guide for Hibernate 3.0 that it is possible. But no details are provided. Do I have to modify anything in the mapping files? What about hibernate.cfg.xml?

Thanks,
Julia.

You will need two sets of mapping files since they are not versioned the same (even though they are mostly similar). The libraries have different package naming structure which allows this to occur but having said that you will need to be explicit in class referencing rather than using just an import if both versions are used from the same application class.