I should know this but I don't quite know it all yet. What would be the standard way for showing topo of a bridge where you have levels/contours above and below. Two separate drawings in AutoCad and print?
Two separate surfaces is one way. Other way is to strip the bridge deck out of surface.
I have always created a separate surface for the deck, and depending on the deliverables, altered its surface style to display contours in a different way. Sometimes you can get away with simply showing the deck linework and a couple of spot elevations of the decking.
was the elevation view (bottom drawing) generated from software or was it manually done?
All automated - Civil 3D (except for the man and the piers, which are blocks and so don't move relative to the elevation, if the elevation extents change they need to be moved). One way to regard Civil 3D is that it is just AutoCAD (until a year or so ago it was called AutoCAD Civil 3D, now it is called just Civil 3D) with a whole lot of utilities that automate what you could manually draw (but wont be dynamic) in AutoCAD.