Separate Everything Into Two Parts
When a 2-D still is completed, it is given to the animation teams who will then draw the mesh over it to animate the image. The mesh is what you find in 3-D tools like autodesk 3d, Maya, and 3dStudio Max. The animators will take this 2-dimensional photograph or scene or whatever, and trace over it for the objects that are supposed to move. When you have the option of creating a scene and adding to it, you can find out whether or not items in it can move.
Some people who are really really good at this will start with Autodesk 3d or whatever tool, and they'll draw all the 3-dimensional spaces, and then someone else will colorize them. Whichever task you want to do is up to you in terms of 3-D modelling.