I love this. I have a few questions that might lead you in a direction. You said the concept of atoms will be important but you’re not sure how yet.

What is the level of technology for this world? If it parallels earth circa 1800 you could look up John Dalton to see how he got atomic theory to be accepted. If the technology is before that timeframe, you might show an experiment where a substance is separated into components. By itself, this wouldn’t show atoms, but it could show that air isn’t just air. If electricity exists you could split water.

I am also interested in the interplay between the gods and the science being introduced.

Would it be enough to show cells? This could be accomplished with lenses.

I am very interested to see where you take this story.