All of the configuration files for Pion are stored as XML within the "config" subdirectory of the main installation directory (or "/etc/pion" on Redhat Linux). Note that vocabulary configurations are stored within a "vocabularies" subdirectory, and SSL keys used to decrypt traffic are stored within an encrypted (binary) "keystore.db" file. The state of these files is consistent unless a configuration change is actively being made via the UI or web services, so you should be able to back everything up by just creating a simple copy of everything in there.