Shape has a very specific meaning in Anime Studio. It means a collection of points in the same vector layer, that share a common line and fill (fill color, fill effect 1 and 2, line color, line width, brush type, and line effect). This is something different from the shape you're used to in drawing, where it is more related to a fill with a border.
For instance, I created this collection of points and gave it two Shapes. The flesh colored shape is one, and the green colored shape is the second. It simply comes down to what points you select when you create a Shape. These selected points then form a Shape, which have the same line and fill features, but don't necessarily looks like the shapes we're used to. "Shape" in AS is a specific term, which has a specific meaning.
This means that
when in one shape, some lines cover other ones
makes no sense, because all lines in one Shape have the same color, so you cannot know which line is on top of another. They are all drawn at the same level.
You can see it this way. There are points, which are connected to other points. Then there are segments, which are connected points in uninterrupted order. Then there are curves, which are connected points with one or several segments. If there are more segments, the curve is branched. Then a vector layer can have several curves on it.
On top of this, and somewhat independent, there are Shapes. You select points in a vector layer with the Create Shape tool, and assign a fill and line to them. If the points form a closed shape, this shape is filled. Note that I used "Shapes" to denote the AS way of forming shapes, and "shapes" to denote what we normally call shapes.
Anyway, see what happens if you put a curve with a Shape assigned to it at the same screen location as another curve with the same Shape assigned to it:
The fill disappears. Where there was color, there is none. You can also see that the flesh colored Shape was put on top of the green colored Shape.
See what happens in this case if you put a third Shape underneath this "hole". You can observe that the hole is indeed a hole (the absence of a fill in that area of the flesh colored Shape).
You can use this loss of fill to your advantage. Suppose you have a face and want to create a mouth into, controlled by bones. If you simply put the mouth shape inside the face and create a Shape, it is hard to control the mouth with a bone. However, if you offset the mouth shape, bind the face with a bone and the mouth with another bone, and use Offset Bones to put the mouth inside the face, you suddenly have full, independent control over the form of the mouth.

(source:
teeth.moho.zip)
In the animation I added a second Shape below the flesh colored Shape on the mouth curve, which was black. The upper and lower teeth are each seperate Shapes, so that when they overlap, they don't cancel out each other's fill.
Of course, in this case (I used point binding instead of region binding) I could have done without Bone Offset, but if for some reason you don't want that, you can use this trick.
Here's an example without Bone Offset:

(source:
teeth2.moho.zip)
I've also added some point animation in some of the frames (point motion and curvature).