GA IFR in US: Manually dialed in.
You file the flight plan (make a proposal/request to ATC) then the request gets processed by ATC in the background.
Then you call for clearance delivery. You write down what they tell you which may be exactly what you proposed (“cleared as filed”) or something different.
Then you manually dial it in with knobs.
In the sim, there is no “filing” with ATC. Except through world map (or import via simbrief or other). For realism, you may want to generate plan in world map (“filing the plan”), write down your flight plan. Then start the plane from cold and dark. Delete the plan in the GPS. Call clearance delivery who will tell you “cleared as filed.” Then manually dial it back in, waypoint by waypoint, start to finish.