I tried positioning them in the environment, but everytime I leave and come back, everything is strewn about like I used Unrelenting Force on it or something.
Ah, yes this is the thing.
The game doesn't take it very well if you place over 9000 items in one go.
Also pro tip, go into your house, drop all the stuff you intend to display on the floor.
Leave house, go get a mead or something at the Mare.
Reenter house... pick up and place objects.
90% of the time this makes objects "settle" in their positions for me.
I also save manually after I've placed any objects.