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When you use a compositing application, you will render your additional 3-D elements "against black", ie with no background image. When you render, you must ensure that your images are not shown in the back of the renders. You may need to disable the background, or set that mesh as "not seen by the camera," depending on your application.
Your renderer will produce an alpha channel that shows the newly rendered pixels and is used to overlay the 3-D imagery over the original images.
For example, you can get this in Fusion by disconnecting the image loader from the input to the Camera3D node, or by un-checking the Enable Image Plane checkbox on the Image tab of the Camera3D node.
With the 3-D portions of the scene rendered against black, then you composite the rendered images over the original images. Again in Fusion, you can connect the final Renderer3D node to a Merge as the foreground, and the original imager to the
background input of the Merge. (Use the output of the Custom nodes if undistortion and redistortion nodes are present.)
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