You usually don't model the character naked. You model him with the clothes on all in one mesh. Unless he is going to take off his clothes or something of that sort. Also, you are going to have problems if you animate both of the clothes and skin. They are going to overlap as the move or as we call it "Cliping".
On the cape. You model the cape horizontally to the ground while attached to the neck. You then make it a live cloth, soft body or you can apply joints. You get a better deformation doing it this way.