Engines are the back-end processes that are run by either cron (for Linux) or scheduled tasks (for Windows). They are responsible for tasks such as polling interfaces, SLA checking or setting alarms and events.
All engines need to be run from the engine directory. On Linux this is usually /opt/jffnms/engine and on Windows it is c:\jffnms\engine. The programs may run outside this directory but there is no guarantee.