General ques. About bones

Hello all. Im a begginer when it comes to animating. I took a basic course at toon boom 7 and now id like to start creating short clips. First problem i encountered is this: when creating a character i must use the z space. E.g i draw a head, so the eyes layer will be a bit closer to camera or it wont show up when rendering. The problems start showng up when i move the camera in my scene, all the character layers start to look very weird because of that z-space method that i use. Problems getting worse when using bones. Now ive seen in the toon boom library examples of a skeleton that all his layers are in the same z-space and it looks As if all his parts were drawn at the same layers far away from each other and then by some magic its all got glued together and the skeleton looks great and can walk. It got something to do with envelope mode i guess. Anyway i know im doing something bad here. I just like a direction on how to start doing things right, not the actual step by step but the idea would help me. Appriciate all answers that you very much in advance.

The basic principle for the order in Time Line is that top most layer in Time Line shows front most in Camera as long as all the layers are in the same z-axis. This however will be overridden by the z-value of the layer.
So it might be a good idea to order the layer in Time line without changing the z-values when rigging the character. For example, eye, nose, mouth layer should be higher in position compare to face in Time Line to be shown front of face in Camera. Also it is good idea to group them together (ex, put all under face upper peg so that you can move all the face at the same time using that peg if needed). Then continue arms, body and legs in order. Then, in general, when you move the arm, the arm will be shown in front of body. When there is any situation the arm has to be behind the body when it is bent, you can use the z-values of the peg (lower arm peg for example) temporary on that frame in period without changing a layer order in Time Line which makes your life much easier. This is also one of the reason for some animator rigs in hierarchy for the arms and legs (or sometimes eyes/eyebrows).
I hope this makes sense to you.