Sky vector is world wide at least low and hi IFR maps . Sectional charts there might be a gap in certain parts of the world. As for the markers it can really be anything. a waypoint a VOR a direct as the bird flies route. Think of it as a regular road map you picking the roads and streets in the sky to fly over. You can go to simbrief first and let that generate route for you between any two larger regional airports and then reverse engineer it in sky vector to see how it was done. Or you can just stick to the highways ie Airways those are the black lines crisscrossing the map and pick low Victor airways that lead you from point A to point B. Each Airway will have an entry and exit points just like a highway and major interchanges around VORs where multiple highways merge just like VOR so in Garmin you plug direct to the closest airway entry waypoint then go to menu load airway pick airway and the exit waypoint and rinse and repeat until you get closer to the destination airport and from there you pick approach routing if airport has a published approach anywhere. Navigraph is a bit more user friendly for manual planning like that. But all of them is really no different in principle than in game map if you were to do it manually. Only in game map is a gamified and skyvector and others are real world. As far as ATC goes I would just turn it off for now. Learn one thing at the time. You only need ATC to cheat around airport if you want to see fly thru landing gates. Don’t over load yourself with too much information.
I would learn map route planning. first From there I would learn how to read operational flight plans from simbrief like LIDO. After that I would learn different methods of navigation, radio navigation GPS navigation different types of approaches. Of course all throughout practice your hand flying skills turns, circuits landings, stalls etc. After that graduate to proper voice controlled ATC program and then maybe fly on VATSIM :).