Clips aren't layering.

I am VERY new to AE, and want to use it mainly for manga animation. I've watched around 8 hours of tutorials, and none i've seen have shown a resolution to the problem I'm having. When I put a clip in the comp, it plays fine, but if i add another clip on top of it, they both won't show up unless one ends so the next can begin. (yes, the shy button is disabled). If I overlap clips, only the one on the bottom shows up, and the one on top won't. When i use the pen tool to create masks, underneath the mask is just my background color, and not the clip that's supposed to be under it. They won't layer.