There's a website i know called Minersneedcoolshoes.com that has a layering feature so you can either put multiple parts on top of others. I have only seen this option on MNCS, but nowhere else.
I think that the PMC editor should have this option so it is easier to make skins. it will also be an interesting way to edit skins and make new ones altogether. it would also be a very interesting feature to add in itself :)