No problem, a picture's worth a thousand words!
The puppets parts follow the order of the layers in the source document, so if you re-order the layers there, Character Animator will honor that order. Note this means that the left leg is always in front of the right or vice versa, so you'll want to consider carefully which order you choose.
There's some additional information here including some suggestions on a workaround for supporting situations when you want multiple orderings.
Thank you for your help!