One of the things we do in the mechanics semester of the Matter &
Interactions curriculum is spend a lot more time than is usual on
"energy-level diagrams" in the classical context of gravitational and
electric potential energy situations, before discussing them in the
atomic/molecular context. This seemed to help my high school physics
teachers a great deal.
We also make a big investment in the notion of "system" and how the choice
of system affects the form of the energy equation. Just last week I
reviewed a paper that was quite garbled, specifically due to the author
never using the word "system" anywhere in the paper.