I have the Topo USA software and I can tell you that it is useful as a tool, but not as a primary source of maps to use in the field. It doesn't have a wide enough field of view to be useful when the map is magnified to the point to see 20ft countour lines, and when you zoom out to see a broader area, the contour lines go out to 100ft which doesn't give you a very good "lay of the land".
I get all my topo maps from
http://www.mytopo.com They also have aerial photos.
I do use the "3d" function of Topo USA but in conjunction with a real topo map at my side. You can zoom in on a point of interest and go to 3d to get a feel for the landscape.
It is also useful in conjunction with a gps for creating and uploading of routes/waypoints, as well as measuring your route and showing you the difficulty of the route by looking at the elevation profile (looks like a lie detector graph showing the elevation of the route you have planned over distance).
If you are new to backcountry navigation off trails, I would first start out in a relatively safe area with varied terrain (by safe I mean fairly small landlocked by roads/railroads or trails). You do need to have some variation in elevation. Get a good topo map of the area and attempt to navigate by "reading" the contour map to determine your position. This will help you see what the landscape should look like when reading the map. You can also use compass to take bearings off 2 known landmarks and draw them on your map. Where they intersect should be your position. You can do this with 1 bearing only if you have an altimeter and know your approximate position already. Where the line intersects the contour line for your elevation is your position.
It is much easier with gps, but you must know how to at least use the compass as gps is not always reliable. Batteries go pretty quick, and if you are under heavy foliage, you won't be able to get a sattelite signal.