It's common to have the front limb lit and the back limb in shadow in these cases. You don't really need full-on detailed shading for small sprites, using the values to instead define the major forms and overlap works quite well. Also, worry about optimizing the colours when you're adding the final colours. While experimenting with the animations, it's fine to keep things flat so you can iterate faster on the animations.
Overlapping limbs of the same colour are also not necessarily a problem, because the rest of the animation can provide the necessary context for the animation to read well. In animation, the clarity of the animation as a whole >>> the clarity of individual frames.
