Back up the entire vault folder, which contains both project documents and Workgroup PDM configuration information. You should do the backup operation when no one is modifying the vault (checking in documents, changing ownership, and so on). To ensure no one is accessing the vault, first lock the vault (see Vault Settings) or stop the service. You can then copy the vault folder with Windows Explorer.
Back up the vault regularly, and test the backup occasionally to be sure your backup procedure is valid. Store the backup on a server different from the one where the vault resides (in case the vault computer is lost).