When it comes to technical documentation, use separate .pod or plain-text files for your external documentation, design documents, data dictionaries, algorithm overviews, change log, and so on. Make sure that the "See Also" section of your user documentation refers to these extra files.
Use comments (and "invisible" POD directives) for internal documentation, explanations of implementation, maintenance notes, et cetera. The following guidelines give details on each of these points.