Hi Citu,
CyAnimator interpolates transitions between key frames that you define. This is typically applied to a single network that has some change in a visual property or positioning of a set nodes or edges. When you say “different networks”, I’m not sure that makes any sense, unless you simply be two different versions of the same network.
If the nodes and edges in the key frames don’t overlap at all (in terms of their identity), then you’d expect the second frame to simply be added to the first, which sounds like what you are seeing.
Obviously, to be more helpful, you’ll need to provide more details about what you are trying to do, exactly what you’ve tried, and what the outcome has been (e.g., cys, screenshots or movie files).