How do Pilots Actually Setup a Flight Plan?

How is that? You don’t file a runway, departure or arrival route, those are not part of the filled flight plan. Furthermore, ATC does not approve the flight plan, the FPL is approved by the Eurocontrol IFPS server. There is little to no human intervention when it comes to filling flight plans. The server just checks the filed route against the Route Availability Document, and minimum and maximum levels for that route. Usually there is a SID for each runway to the same start of en-route segment. Same for the STAR, there usually is a STAR from the same termination point to the IAF for the respective runway. If not, ATC will amend your flight plan by means of RTF or CPDLC.