DISCLAIMER: I'm not adept with programs like these and I have a very VERY basic understanding (if at all) of what I'm doing, so I apologize if my choice of words is poor or incorrect; bear with me, please.
I'm making a puppet in AI CS5 to be used for an animation in AE CS5. Because it is hand-drawn, I've used the pen tool to fill shapes. I have each leg in its own respective layer and I've created a "pelvis" layer for the legs to be attached. I'd like the character to look as though he wearing pants, so I don't want the top of the leg shape to be seen and I've moved the legs behind the pelvis.
If I parent the "thigh fill" to the leg while in AE, it does the trick. It stays with the leg and that's great, but that means anytime I have an overlap that needs to be corrected, I have to make a new layer. So my question is if this is a bad way to do this or is there a better, cleaner way to cover areas such as these and keep them covered as parts of the character move around?