You can also use pilotage and dead reckoning to get comfortable with navigating. Use local landmarks to get an idea of where you are and where you should be. In actual training, you learn to fly using landmarks, and using your heading with wind correction to navigate before you learn to use VORs (I did at least). If you were planning and flying an actual cross country flight, you would take a marker and draw your course on a sectional, and find checkpoints (lakes, river bends, hills, etc...) every ten miles or so, so when you fly over a checkpoint, you can see, "oh, I'm on the south side of this lake instead of the north side, I should fix that...", that way, when you get close to your destination, you should be able to find it. You can use
http://skyvector.com/ for sectionals to use in Flight Simulator (only FS!). You can also get the winds aloft in the FS weather window, and then use that information to find your actual course with wind correction, and your time between checkpoints, then you can time yourself between each checkpoint, then you should be able to time yourself to your destination and be pretty close again. You can use
http://www.csgnetwork.com/e6bcalc.html as a flight computer to find wind correction angles and speeds.