How can I edit a scene at runtime and have those variables saved?

So I have a scene with a bunch of objects placed. I want to be able to move them around at runtime and then when I stop the game, keep those values. Just to help get the scene where I want it to be. All my objects are created at runtime based of initial positions.

One way I can get it to work is have a prefab. move the stuff around and then save that object into the prefab again. Is there a better way to do this?

There are a few things that I know of but never tried myself, unfortunately most of them you have to pay for:

AngryAnt - CopyInspector (Apprently with this one you can copy components at runtime and then paste them in the editor afterwards).