PaperDoll works with any 2D scenario where you are working with multiple paper doll layers but also works for changing our like sprites. So let's say for example, you were making a shmup and you had five Sprite sheets of different ships but they all had the same number of sprites for their animations. You could then make one set of animations rather than five sets of animations and just use paper doll to switch between all the different sets. Also, there is a video that shows how to set up paper doll if that is easier.
Please let me know if you continue to have issues in which case we could do a remote session to help you get it set up.