Since Andrew asked me to join him and the Pixar guys who teach at the Academy, and then Spline Doctors, the one thing that I've seen most consistently asked of students is advice on work method. Now, I'm a 2D guy. Not including one shot I did on IRON GIANT, INCREDIBLES was my first experience with 3D. I'm the least tech savvy of the fellows who started this blog (and for that matter, probably of the people I work with), but I figured it was about time I faced some of my fears and ventured forth from the safe harbor of my previous posts regarding performance and address some of your questions regarding 3D work method. Bear in mind, there are people far more talented than I who can address some of these issues, but I figured if an approach can work for someone like me....it can work for anyone.
A question that has come up in recent comments is, "How can I work pose-to-pose and still use a layered approach?" I don't claim to know the answer but I can share with you what has worked for me. First, I can't start a scene without knowing where I'm going. I will thumbnail every scene I get so I have a roadmap of the poses, beats, and attitudes that I know I am going for. I will then pose out my shot to match the thumbnails I've done. Bear in mind that some of these poses are going to be breakdowns of action that will help me map out the transition of movement from pose to pose. The biggest mistake I see students make working pose-to-pose in 3D is not thinking about the actual movement. They get lost in the poses and forget about the animation. I will then time out the shot with a series of holds not unlike on old-school, 2D pose test.
Once I feel that the overall timing and poses are working, I will immediately go into spline work polishing the main movement in the shot, working from the root, outward. I'll start off by invising geometry that might distract me (i.e. arms, legs, etc.) and bring into the spline editor the controls that define the main movement of the shot and start polishing. It may be the root. It may be the chest, neck, and head. It may be just an arm and a hand. Whatever it is, I will work from the inside out and I'll never polish any more than 3 to 4 controls at a time while I'm working in the spline editor. I will then work by tweaking and adjusting my animation and playblasting often. Even though you're working on a computer, animation is a very organic process. Work with your shot so it feels right to you. Don't let the computer dictate what you will accept. If it doesn't feel or look right, keep working at it until it does. If you still don't see it (and don't know how to get there) find someone more tech savvy than you and see if s/he can steer you to what controls you need to manipulate to get the results you're looking for. DON'T TAKE "NO" FOR AN ANSWER.
Once things seem to be moving the way I've envisioned, I will then start re-vising geometry and begin polishing outward. Please bear in mind though, that this approach will work ONLY if you have truly thought out your shot. Your original vision may evolve along the way, but you can't work like this without a clear idea of what you're going for. For that matter, whether it's 2D or 3D, you should never start animating before you know what you're going to do. Good luck and I hope this helped.