I was doing some playing with frames just to verify what is going on. and as far as I can see when you create a new layer it is applied to the last frame only, but if you create a new frame is is copied.
What I did was create 2 layers one a background gradient, second is a raster rectangle.
For frames, the first is the background, second is the rectangle and the third is the same rectangle, now I can click on either frame and move that rectangle.