How do 3D objects coincide with traditional 2D animation? I was watching an episode of Shirobako. I love how the anime gives you a slight in-depth view on the production process. However, something I can't get my mind around is those few segments that involve CGI (in anime in general) with the interaction of traditional 2D animation such as stationary or moving objects.

In the episode, a scene in Exodus where the girls rides a jeep while avoiding explosion was shown in key animations/"genga": http://sakuga.yshi.org/post/show/10903.

As you can see, the 3D bike and characters basically move together on a plane. Could it be that the bike is animated frame by frame in traditional animation somehow? Or the other way around? Or could it be more technical than those?
The bike can be animated in a 3D model editor application and overlayed upon the ready 2D frames. It doesn't really matter which application both come from, since they can all export frames to static images. 3D editors have motion direction, of course, or else we would not see much 3D movies. And you can not add anything else aside from the main 3D mesh with applied texture, so that the background will be transparent upon frame export.  You know how they have those "layers" in Photoshop? Well, that is it. One of them comes from 2D app, the other from 3D. Nothing special.

Images taken from this Autodesk 3ds Max™ tutorial showing how not much of a rocket science it is to create 3D scenes with transparency (click images for full resolution):



The image with transparent background and white shadow with gradual transparency changing, after exporting from a 3D editor, can be imported into a 2D editor (such as Adobe Photoshop) and be laid over some colored rectangles like this:

 

We also have sites like GraphicDesign on StackExchange Questions and Answers sites network that ask questions on similar topics with such illustrations:



You say "traditional animation", but that really means collaging paper elements on a table, taking a shot of the scene and later on gluing together the resulting frames into a cinema roll. You must want to know about the modern day way, so that is what I described above.

Older animation techniques require the use of celluloid sheets, which are transparent sheets of plastic, to make the things simple. Are you familiar with the term cel-shading? Well, this is where the modern day 3D animation technique comes from − the older days method of drawing the outline of objects on a cel sheet. It goes something like this: You draw the black outline and the fill inside areas with colored paint. Then you place it above the scene image and move around or swap for other cels with different character poses.

 

There are a number of techniques used to overlay 3D objects onto ready frames of anything else, used by all sorts of "magicians" in their shows. You could ask google how they did it before computers and find out something new.