New customer-specific classes, classes which wrap existing classes, or in a limited set of circumstances new subclasses of existing classes should be written in new source files. All new source files should be placed within the source subdirectory of the EJBServer\components\custom directory.
For modeled classes, the generated class hierarchy will dictate the package structure of the new source files. See the Cúram Server Developer's Guide for information on modeling new classes and replacing existing implementations.
For handcrafted implementations, it is up to you how the new class is packaged. See the Persistence Cookbook for information on configuring new subclasses using Google Guice.