I am not sure if there is a way to switch automatically between two inputs. There is a "switch back" button, the one under the Discover button showing a circle made with a double arrow, but it doesn't always go back to the previous content (it should wokr between TV channels, though). Then in Android 7 there is the feature that holding Home you can go back to the previous apps. Or you may want to add Amazon Video to the list of Discovery apps in the Discover button.
Still none of this would solve your issue. Amazon Video always restarts once you do something else. It uses an awful load of RAM so I believe Android closes it as soon as we switch to something else. But it shouldn't matter, because Amazon Video does bookmark the last position reached in a movie/episode. And the last video should automatically move to the top of the "Watch Next" section.
That's how it works with me. The Watch Next section sometimes loses some members, but playing them again from other sections the last bookmark is always memorized.
If that still doesn't work for you, you may try to access Amazon Prime Video from the PC web browser. Remember the point you reached on a movie from the TV and if the bookmark is lost, skip to it in the web broswer. Then check if it is memorized on TV. I did a similar thing with the subtitles, since on TV it was always starting showing the German subs. After I selected the English audio and subs from the web it always uses them.
