Aircraft transponders are a part of Secondary Surveillance Radar (SSR). These transponders reply to interrogation from a ground station with a code set by the pilot and instructed to do so by air traffic control.
Instructions for filling out a flight plan for an aircraft equipped with a mode S transponder can be found in the document below.
How to fill out a flight plan with mode S according to EuroControl.
Excerpt from the document:
European States will be commencing Mode S ELS services in the near future but, of course, ATC ground surveillance and flight plan processing systems need to be fully tested beforehand. Although this process has already begun, we need YOU, flight crews and aircraft operations staff, to accurately complete flight plans and operate your Mode S transponders in the approved manner. Only then can the systems be validated for operational use.
It is imperative, therefore, that the following, simple steps (as detailed in ICAO Doc 4444 – Procedures for Air Navigation Services: Air Traffic Management and ICAO Doc 8168 - Procedures for Air Navigation Services: Aircraft Operations) are followed precisely.
To continue reading see the pdf below: