1 - Add the image or clip to overlay as an additional camera, and set its compose mode to "Overlay",

2 - Set its mapping to rectilinear if you want to make it flat. 

3 - Use its yaw/pitch/roll parameters to place it, and change its focal length to scale it. 

4 - For additional control, use its lens center to shift it left-right or up-down along its plane. 

Note: For the case of Stereo 3D, first adjust one of the eyes, like the left one. When you are done, add the image for the right eye, and copy / paste all the parameters that you modified so it appears in the same place. Finally, set the cameras "stereo eye" to left and right, respectively.