Now, I have the basics down, (I think) and i'm still messing around, but I was wondering,
when you make a new character, and the character has over lapped body parts, how do you spread them out and add bones, and when you start animating they come together to form the character. I don't know if I made that sound confusing, but i'll demonstrate.
this character (below) has overlapping body parts:

He's spread out, so that the body parts don't get confused
When you press play, he comes together like this:

Now, how do I go about making my own character like that?