Automatic ChangeLogs mode is the default. Each time you (re)generate a diff, Patcher (re)creates ChangeLog skeletons in the appropriate ChangeLog files, by analyzing the generated diff. You then need to fill the entries manually.
Note that when Patcher creates skeletons for you, you should never kill the ChangeLog buffers while a project is running. Otherwise, Patcher will loose track of what it has or has not generated.