You may wish to give a chance to kdenlive, which includes several keyframable plugins like those you may need in order to do that work.

It comes to my mind the track plugin "MaskOMate" to "cut" the part of the image that you wish to put overlaying the video. Of course, it will be useful if you first prepare the images in order to fit the project's size, with transparency, then simply use the "Composite" track's transition in order to put the images over the video.

Both "MaskOMate" and "Composite" plugins are keyframable, so you can choose where to place your video elements in a certain moment of the video play.

See the official kdenlive site and the Creative effects page for further information.

In the next screenshot, I am using a pre-made transparency image with an amazed girl in order to place it on the background video where a man is appearing over a green screen wall. Of course, I also used the "Pan and Zoom" Plugin in order to make the image bigger. Remember: The best your sources are, the best results you'll get.

What you wish to achieve is complicated and a hard work but with patience and creativity you can create an awesome video.

Good luck!