Workflows

Live footage only:
Once a digital format of the footage is obtained editors would normally edit a 'rough cut' with editing softwares, Final Cut Pro, Premiere or Avid for example, in order to mark out the footage that is definitely going to be used, also giving a basic structure of the piece. This is called an offline edit. The edit is then brought into compositing softwares like After Effect, Nuke or Smoke for motion graphics, special effects and shot finesse. Music and sound could be placed at this stage for experiment sake but I would not recommend it. Composited footage is then brought back into the editing softwares for more advanced editing like colour grading, where you adjust the colours and contrast of each shot to make them blend in together. Sound effects and music are then added for the final edit. The final version of the edit is called 'final cut'.

Live footage and animation:
The workflow really depends on the type and style of the animation as well as how it is being incorporated with live footage, this thus requires more planning. However, it is essential to shoot the live footage first, as CG elements are easily manipulatable, and to know where the animations will be when you are shooting. This is when storyboards and animatics play a crucial part in the production.
Following the workflow of live footage above, a 'rough cut' is required to pick out the footage that is going to be used. This is then used as a reference for animators to place in the 2D animation or rotoscoping effect.
When 3D elements are involved however, tracking softwares like MatchMover, Voodoo and PFTrack are required to match up the CG cameras with the footage. This way the perspective of the CG characters and environment could match up with the live footage. When 3D elements are animated and rendered out, they are then composited together for the 'final cut'.

Through 'dynamic link' we are able to transfer assets, edits and effects into various softwares at different stages, this greatly increases the production speed because the rendering stage is only required at the very end of the pipeline. However, I will not go into details about that in this tutorial. Google?