For now the generation overwrites content.
You can specify which entities you want generated via reveng.xml.
Customization of what type of files you want generated is editable if you go to Run > Hibernate Code generation and edit the properties of the "generate entities" launch. (if you want the changes to stay around copy the launch and use the copy as the original gets updated when you run the seam generate entities wizard)
About what all the files do I would recommend you read the Seam documentation about pages.xml navigation and/or ask on the seam forum.
Thanks a lot Max!
Just in case someone else needs:
In the Hibernate Code Generation Dialog, the Main tab allows you to configure the set of entities you want to generated code for, by creating an hibernate.reveng.xml file. Afterward, this file can be edited as a normal xml file with a couple of helpful specific views.
At the Exporters tab, there is a list of exporters. Each one of these, are a template that describes one of the files that are to be created. So one describes how the ClassNameList.xhtml is going to be created, and other, has the description for ClassNameList.page.xml.
This is just a 10000 m view over the most important features you could configure here, but there is plenty to learn still.