Hi Lewis,
Let me add a few details to Dom's explanations...
1. Propilot flights require using the FlightLogger, but the FlightLogger is not only useful for Propilot Flights. For any flight, it provides a way to record the flight and submit it immediately, instead of submitting a PIREP form only and depend on MT validation

2. In the folder where the FlightLogger installs, you can find a PDF manual that explains much of its functions.
3. You must have the FSUIPC module properly installed when you start the FlightLogger for the first time, in order to have it "locate" where the FS is installed. Otherwise you will keep getting the "Can't connect to FS" message.
4. When downloading FSUIPC, pay attention to the versions because there is always a "FSX current" and a "Fs9 current".
5. When you have everything up and running, AND a Propilot flight locked, DO NOT choose this flight in the FlightLogger. Instead, use the "ProPilot" button on the timetable page, which will automatically pick your locked flight.
6. I am not sure about this one but it's possible that you cannot use FlightLogger as long as you don't have your definitive (all-digits) EHM ID. From my beginnings two years ago I remember recording my first ever EHM flight by web form PIREP. But again, I may be wrong on this one...
Hope this helps
Andrei