There are a couple of different ways to navigate using maps.
If you want to navigate using roads and rivers then Cpirrmans recent posts in another thread cover it well:
The maps on Polovski's sight are good but inaccurate. The best ones are from MS Encarta's web site. The roads, rivers, railroads and towns are 99.9% accurate with WM's scenery...I take fine point markers and enhance the details. Orange for roads, green for rivers, and black for RR's. I keep them in plastic sleeves and use grease pencils to mark landmarks, airfields, army bases, balloons etc, as I spot them. If you fly the region long enough, you'll get to know it like the back of your hand. IRL, we fly with accurate charts that we mark up.
Myself, I navigate using only the airfields, cities and the frontline for references because these are all really easy to see from long distances. At the first mission briefing of a campaign I will usually just hand sketch a simple paper map of these features based on the CSF3 briefing map. Another good option is to use FRAPS to capture and print the CSF3 briefing map.
As Cpirrman says above, after a few flights you rarely need the map anymore as you have learned the local area.