I can't seem to get smart objects into layers of a single file, as I can do if instead I use normal images. I use the move tool to move an image to another file and this creates them as layers of this targets file. However when the images are instead smart objects and I try to move one to the other, the image moves out of its frame and I cannot place it into the other smart object.
It sounds like you do not know how to do something. Post some screen captures to show the problems you are having. When you place in an image there is a Place transform for each smart object layer placed into the documeny. That lets you Size and position the image anywhere you want it to be in the documents composite.